[805] | 1 | // |
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| 2 | // C++ Implementation: Scantable |
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| 3 | // |
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| 4 | // Description: |
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| 5 | // |
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| 6 | // |
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| 7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005 |
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| 8 | // |
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| 9 | // Copyright: See COPYING file that comes with this distribution |
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| 10 | // |
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| 11 | // |
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[206] | 12 | #include <map> |
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| 13 | |
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[2186] | 14 | #include <atnf/PKSIO/SrcType.h> |
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| 15 | |
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[125] | 16 | #include <casa/aips.h> |
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[2186] | 17 | #include <casa/iomanip.h> |
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[80] | 18 | #include <casa/iostream.h> |
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[2186] | 19 | #include <casa/OS/File.h> |
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[805] | 20 | #include <casa/OS/Path.h> |
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[80] | 21 | #include <casa/Arrays/Array.h> |
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[2186] | 22 | #include <casa/Arrays/ArrayAccessor.h> |
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| 23 | #include <casa/Arrays/ArrayLogical.h> |
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[80] | 24 | #include <casa/Arrays/ArrayMath.h> |
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| 25 | #include <casa/Arrays/MaskArrMath.h> |
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[2186] | 26 | #include <casa/Arrays/Slice.h> |
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[1325] | 27 | #include <casa/Arrays/Vector.h> |
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[455] | 28 | #include <casa/Arrays/VectorSTLIterator.h> |
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[418] | 29 | #include <casa/BasicMath/Math.h> |
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[504] | 30 | #include <casa/BasicSL/Constants.h> |
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[2186] | 31 | #include <casa/Containers/RecordField.h> |
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| 32 | #include <casa/Logging/LogIO.h> |
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[286] | 33 | #include <casa/Quanta/MVAngle.h> |
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[2186] | 34 | #include <casa/Quanta/MVTime.h> |
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[902] | 35 | #include <casa/Utilities/GenSort.h> |
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[2] | 36 | |
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[2186] | 37 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[2] | 38 | |
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[1325] | 39 | // needed to avoid error in .tcc |
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| 40 | #include <measures/Measures/MCDirection.h> |
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| 41 | // |
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| 42 | #include <measures/Measures/MDirection.h> |
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[2186] | 43 | #include <measures/Measures/MEpoch.h> |
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[80] | 44 | #include <measures/Measures/MFrequency.h> |
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[2186] | 45 | #include <measures/Measures/MeasRef.h> |
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| 46 | #include <measures/Measures/MeasTable.h> |
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| 47 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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| 48 | #include <measures/TableMeasures/TableMeasDesc.h> |
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[805] | 49 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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| 50 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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[2] | 51 | |
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[2186] | 52 | #include <tables/Tables/ArrColDesc.h> |
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| 53 | #include <tables/Tables/ExprNode.h> |
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| 54 | #include <tables/Tables/ScaColDesc.h> |
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| 55 | #include <tables/Tables/SetupNewTab.h> |
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| 56 | #include <tables/Tables/TableCopy.h> |
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| 57 | #include <tables/Tables/TableDesc.h> |
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| 58 | #include <tables/Tables/TableIter.h> |
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| 59 | #include <tables/Tables/TableParse.h> |
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| 60 | #include <tables/Tables/TableRecord.h> |
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| 61 | #include <tables/Tables/TableRow.h> |
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| 62 | #include <tables/Tables/TableVector.h> |
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| 63 | |
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| 64 | #include "MathUtils.h" |
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| 65 | #include "STAttr.h" |
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| 66 | #include "STLineFinder.h" |
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| 67 | #include "STPolCircular.h" |
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[896] | 68 | #include "STPolLinear.h" |
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[913] | 69 | #include "STPolStokes.h" |
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[2321] | 70 | #include "STUpgrade.h" |
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[2186] | 71 | #include "Scantable.h" |
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[2] | 72 | |
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[2462] | 73 | #define debug 1 |
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| 74 | |
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[125] | 75 | using namespace casa; |
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[2] | 76 | |
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[805] | 77 | namespace asap { |
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| 78 | |
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[896] | 79 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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| 80 | |
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| 81 | void Scantable::initFactories() { |
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| 82 | if ( factories_.empty() ) { |
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| 83 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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[1323] | 84 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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[913] | 85 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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[896] | 86 | } |
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| 87 | } |
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| 88 | |
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[805] | 89 | Scantable::Scantable(Table::TableType ttype) : |
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[852] | 90 | type_(ttype) |
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[206] | 91 | { |
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[896] | 92 | initFactories(); |
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[805] | 93 | setupMainTable(); |
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[2346] | 94 | freqTable_ = STFrequencies(*this); |
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| 95 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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[852] | 96 | weatherTable_ = STWeather(*this); |
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[805] | 97 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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[852] | 98 | focusTable_ = STFocus(*this); |
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[805] | 99 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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[852] | 100 | tcalTable_ = STTcal(*this); |
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[805] | 101 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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[852] | 102 | moleculeTable_ = STMolecules(*this); |
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[805] | 103 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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[860] | 104 | historyTable_ = STHistory(*this); |
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| 105 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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[959] | 106 | fitTable_ = STFit(*this); |
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| 107 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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[1881] | 108 | table_.tableInfo().setType( "Scantable" ) ; |
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[805] | 109 | originalTable_ = table_; |
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[322] | 110 | attach(); |
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[18] | 111 | } |
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[206] | 112 | |
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[805] | 113 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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[852] | 114 | type_(ttype) |
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[206] | 115 | { |
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[896] | 116 | initFactories(); |
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[1819] | 117 | |
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[865] | 118 | Table tab(name, Table::Update); |
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[1009] | 119 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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[483] | 120 | if (version != version_) { |
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[2321] | 121 | STUpgrade upgrader(version_); |
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[2162] | 122 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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| 123 | os << LogIO::WARN |
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[2321] | 124 | << name << " data format version " << version |
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| 125 | << " is deprecated" << endl |
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| 126 | << "Running upgrade."<< endl |
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[2162] | 127 | << LogIO::POST ; |
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[2321] | 128 | std::string outname = upgrader.upgrade(name); |
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[2332] | 129 | if ( outname != name ) { |
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| 130 | os << LogIO::WARN |
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| 131 | << "Data will be loaded from " << outname << " instead of " |
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| 132 | << name << LogIO::POST ; |
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| 133 | tab = Table(outname, Table::Update ) ; |
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| 134 | } |
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[483] | 135 | } |
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[1009] | 136 | if ( type_ == Table::Memory ) { |
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[852] | 137 | table_ = tab.copyToMemoryTable(generateName()); |
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[1009] | 138 | } else { |
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[805] | 139 | table_ = tab; |
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[1009] | 140 | } |
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[1881] | 141 | table_.tableInfo().setType( "Scantable" ) ; |
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[1009] | 142 | |
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[859] | 143 | attachSubtables(); |
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[805] | 144 | originalTable_ = table_; |
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[329] | 145 | attach(); |
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[2] | 146 | } |
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[1819] | 147 | /* |
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| 148 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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| 149 | type_(ttype) |
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| 150 | { |
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| 151 | initFactories(); |
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| 152 | Table tab(name, Table::Update); |
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| 153 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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| 154 | if (version != version_) { |
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| 155 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 156 | } |
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| 157 | if ( type_ == Table::Memory ) { |
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| 158 | table_ = tab.copyToMemoryTable(generateName()); |
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| 159 | } else { |
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| 160 | table_ = tab; |
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| 161 | } |
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[2] | 162 | |
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[1819] | 163 | attachSubtables(); |
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| 164 | originalTable_ = table_; |
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| 165 | attach(); |
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| 166 | } |
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| 167 | */ |
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| 168 | |
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[2163] | 169 | Scantable::Scantable( const Scantable& other, bool clear ): |
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| 170 | Logger() |
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[206] | 171 | { |
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[805] | 172 | // with or without data |
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[859] | 173 | String newname = String(generateName()); |
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[865] | 174 | type_ = other.table_.tableType(); |
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[859] | 175 | if ( other.table_.tableType() == Table::Memory ) { |
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| 176 | if ( clear ) { |
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| 177 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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| 178 | other.table_, True); |
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| 179 | } else |
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| 180 | table_ = other.table_.copyToMemoryTable(newname); |
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[16] | 181 | } else { |
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[915] | 182 | other.table_.deepCopy(newname, Table::New, False, |
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| 183 | other.table_.endianFormat(), |
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[865] | 184 | Bool(clear)); |
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| 185 | table_ = Table(newname, Table::Update); |
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| 186 | table_.markForDelete(); |
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| 187 | } |
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[1881] | 188 | table_.tableInfo().setType( "Scantable" ) ; |
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[1111] | 189 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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[915] | 190 | if ( clear ) copySubtables(other); |
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[859] | 191 | attachSubtables(); |
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[805] | 192 | originalTable_ = table_; |
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[322] | 193 | attach(); |
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[2] | 194 | } |
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| 195 | |
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[865] | 196 | void Scantable::copySubtables(const Scantable& other) { |
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| 197 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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[2346] | 198 | TableCopy::copyRows(t, other.freqTable_.table()); |
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[865] | 199 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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| 200 | TableCopy::copyRows(t, other.focusTable_.table()); |
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| 201 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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| 202 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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| 203 | t = table_.rwKeywordSet().asTable("TCAL"); |
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| 204 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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| 205 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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| 206 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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| 207 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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| 208 | TableCopy::copyRows(t, other.historyTable_.table()); |
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[972] | 209 | t = table_.rwKeywordSet().asTable("FIT"); |
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| 210 | TableCopy::copyRows(t, other.fitTable_.table()); |
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[865] | 211 | } |
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| 212 | |
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[859] | 213 | void Scantable::attachSubtables() |
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| 214 | { |
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[2346] | 215 | freqTable_ = STFrequencies(table_); |
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[859] | 216 | focusTable_ = STFocus(table_); |
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| 217 | weatherTable_ = STWeather(table_); |
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| 218 | tcalTable_ = STTcal(table_); |
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| 219 | moleculeTable_ = STMolecules(table_); |
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[860] | 220 | historyTable_ = STHistory(table_); |
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[972] | 221 | fitTable_ = STFit(table_); |
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[859] | 222 | } |
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| 223 | |
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[805] | 224 | Scantable::~Scantable() |
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[206] | 225 | { |
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[2] | 226 | } |
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| 227 | |
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[805] | 228 | void Scantable::setupMainTable() |
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[206] | 229 | { |
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[805] | 230 | TableDesc td("", "1", TableDesc::Scratch); |
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| 231 | td.comment() = "An ASAP Scantable"; |
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[1009] | 232 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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[2] | 233 | |
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[805] | 234 | // n Cycles |
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| 235 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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| 236 | // new index every nBeam x nIF x nPol |
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| 237 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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[2] | 238 | |
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[805] | 239 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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| 240 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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[972] | 241 | // linear, circular, stokes |
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[805] | 242 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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| 243 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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[138] | 244 | |
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[805] | 245 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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| 246 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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[80] | 247 | |
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[1819] | 248 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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| 249 | refbeamnoColumn.setDefault(Int(-1)); |
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| 250 | td.addColumn(refbeamnoColumn); |
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| 251 | |
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| 252 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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| 253 | flagrowColumn.setDefault(uInt(0)); |
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| 254 | td.addColumn(flagrowColumn); |
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| 255 | |
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[805] | 256 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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| 257 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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| 258 | TableMeasValueDesc measVal(td, "TIME"); |
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| 259 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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| 260 | mepochCol.write(td); |
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[483] | 261 | |
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[805] | 262 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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| 263 | |
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[2] | 264 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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[805] | 265 | // Type of source (on=0, off=1, other=-1) |
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[1503] | 266 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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| 267 | stypeColumn.setDefault(Int(-1)); |
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| 268 | td.addColumn(stypeColumn); |
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[805] | 269 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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| 270 | |
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| 271 | //The actual Data Vectors |
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[2] | 272 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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| 273 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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[89] | 274 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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[805] | 275 | |
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| 276 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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| 277 | IPosition(1,2), |
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| 278 | ColumnDesc::Direct)); |
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| 279 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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| 280 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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| 281 | // the TableMeasDesc gives the column a type |
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| 282 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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[987] | 283 | // a uder set table type e.g. GALCTIC, B1950 ... |
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| 284 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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[805] | 285 | // writing create the measure column |
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| 286 | mdirCol.write(td); |
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[923] | 287 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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| 288 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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[1047] | 289 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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[105] | 290 | |
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[805] | 291 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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[972] | 292 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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[973] | 293 | fitColumn.setDefault(Int(-1)); |
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[972] | 294 | td.addColumn(fitColumn); |
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[805] | 295 | |
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| 296 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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| 297 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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| 298 | |
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[999] | 299 | // columns which just get dragged along, as they aren't used in asap |
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| 300 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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| 301 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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| 302 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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| 303 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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| 304 | |
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[805] | 305 | td.rwKeywordSet().define("OBSMODE", String("")); |
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| 306 | |
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[418] | 307 | // Now create Table SetUp from the description. |
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[859] | 308 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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[852] | 309 | table_ = Table(aNewTab, type_, 0); |
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[805] | 310 | originalTable_ = table_; |
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| 311 | } |
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[418] | 312 | |
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[805] | 313 | void Scantable::attach() |
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[455] | 314 | { |
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[805] | 315 | timeCol_.attach(table_, "TIME"); |
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| 316 | srcnCol_.attach(table_, "SRCNAME"); |
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[1068] | 317 | srctCol_.attach(table_, "SRCTYPE"); |
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[805] | 318 | specCol_.attach(table_, "SPECTRA"); |
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| 319 | flagsCol_.attach(table_, "FLAGTRA"); |
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[865] | 320 | tsysCol_.attach(table_, "TSYS"); |
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[805] | 321 | cycleCol_.attach(table_,"CYCLENO"); |
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| 322 | scanCol_.attach(table_, "SCANNO"); |
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| 323 | beamCol_.attach(table_, "BEAMNO"); |
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[847] | 324 | ifCol_.attach(table_, "IFNO"); |
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| 325 | polCol_.attach(table_, "POLNO"); |
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[805] | 326 | integrCol_.attach(table_, "INTERVAL"); |
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| 327 | azCol_.attach(table_, "AZIMUTH"); |
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| 328 | elCol_.attach(table_, "ELEVATION"); |
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| 329 | dirCol_.attach(table_, "DIRECTION"); |
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| 330 | fldnCol_.attach(table_, "FIELDNAME"); |
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| 331 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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[455] | 332 | |
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[1730] | 333 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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[805] | 334 | mfitidCol_.attach(table_,"FIT_ID"); |
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| 335 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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| 336 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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| 337 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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| 338 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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[1819] | 339 | |
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| 340 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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| 341 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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| 342 | |
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[455] | 343 | } |
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| 344 | |
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[1819] | 345 | template<class T, class T2> |
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| 346 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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| 347 | const String& colName, |
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| 348 | const T2& defValue) |
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| 349 | { |
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| 350 | try { |
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| 351 | col.attach(table_, colName); |
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| 352 | } catch (TableError& err) { |
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| 353 | String errMesg = err.getMesg(); |
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| 354 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 355 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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| 356 | col.attach(table_, colName); |
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| 357 | col.fillColumn(static_cast<T>(defValue)); |
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| 358 | } else { |
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| 359 | throw; |
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| 360 | } |
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| 361 | } catch (...) { |
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| 362 | throw; |
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| 363 | } |
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| 364 | } |
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| 365 | |
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| 366 | template<class T, class T2> |
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| 367 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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| 368 | const String& colName, |
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| 369 | const Array<T2>& defValue) |
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| 370 | { |
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| 371 | try { |
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| 372 | col.attach(table_, colName); |
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| 373 | } catch (TableError& err) { |
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| 374 | String errMesg = err.getMesg(); |
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| 375 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 376 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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| 377 | col.attach(table_, colName); |
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| 378 | |
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| 379 | int size = 0; |
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| 380 | ArrayIterator<T2>& it = defValue.begin(); |
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| 381 | while (it != defValue.end()) { |
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| 382 | ++size; |
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| 383 | ++it; |
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| 384 | } |
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| 385 | IPosition ip(1, size); |
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| 386 | Array<T>& arr(ip); |
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| 387 | for (int i = 0; i < size; ++i) |
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| 388 | arr[i] = static_cast<T>(defValue[i]); |
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| 389 | |
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| 390 | col.fillColumn(arr); |
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| 391 | } else { |
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| 392 | throw; |
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| 393 | } |
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| 394 | } catch (...) { |
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| 395 | throw; |
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| 396 | } |
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| 397 | } |
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| 398 | |
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[901] | 399 | void Scantable::setHeader(const STHeader& sdh) |
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[206] | 400 | { |
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[18] | 401 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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| 402 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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| 403 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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| 404 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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| 405 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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| 406 | table_.rwKeywordSet().define("Project", sdh.project); |
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| 407 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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| 408 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
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| 409 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
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| 410 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
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| 411 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
---|
| 412 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
---|
| 413 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
---|
| 414 | table_.rwKeywordSet().define("UTC", sdh.utc); |
---|
[206] | 415 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
---|
| 416 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
---|
[905] | 417 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
---|
[50] | 418 | } |
---|
[21] | 419 | |
---|
[901] | 420 | STHeader Scantable::getHeader() const |
---|
[206] | 421 | { |
---|
[901] | 422 | STHeader sdh; |
---|
[21] | 423 | table_.keywordSet().get("nBeam",sdh.nbeam); |
---|
| 424 | table_.keywordSet().get("nIF",sdh.nif); |
---|
| 425 | table_.keywordSet().get("nPol",sdh.npol); |
---|
| 426 | table_.keywordSet().get("nChan",sdh.nchan); |
---|
| 427 | table_.keywordSet().get("Observer", sdh.observer); |
---|
| 428 | table_.keywordSet().get("Project", sdh.project); |
---|
| 429 | table_.keywordSet().get("Obstype", sdh.obstype); |
---|
| 430 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
---|
| 431 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
---|
| 432 | table_.keywordSet().get("Equinox", sdh.equinox); |
---|
| 433 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
---|
| 434 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
---|
| 435 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
---|
| 436 | table_.keywordSet().get("UTC", sdh.utc); |
---|
[206] | 437 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
---|
| 438 | table_.keywordSet().get("Epoch", sdh.epoch); |
---|
[905] | 439 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
---|
[21] | 440 | return sdh; |
---|
[18] | 441 | } |
---|
[805] | 442 | |
---|
[1360] | 443 | void Scantable::setSourceType( int stype ) |
---|
[1068] | 444 | { |
---|
| 445 | if ( stype < 0 || stype > 1 ) |
---|
| 446 | throw(AipsError("Illegal sourcetype.")); |
---|
| 447 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
---|
| 448 | tabvec = Int(stype); |
---|
| 449 | } |
---|
| 450 | |
---|
[845] | 451 | bool Scantable::conformant( const Scantable& other ) |
---|
| 452 | { |
---|
| 453 | return this->getHeader().conformant(other.getHeader()); |
---|
| 454 | } |
---|
| 455 | |
---|
| 456 | |
---|
[50] | 457 | |
---|
[805] | 458 | std::string Scantable::formatSec(Double x) const |
---|
[206] | 459 | { |
---|
[105] | 460 | Double xcop = x; |
---|
| 461 | MVTime mvt(xcop/24./3600.); // make days |
---|
[365] | 462 | |
---|
[105] | 463 | if (x < 59.95) |
---|
[281] | 464 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
[745] | 465 | else if (x < 3599.95) |
---|
[281] | 466 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
| 467 | else { |
---|
| 468 | ostringstream oss; |
---|
| 469 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
| 470 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
| 471 | return String(oss); |
---|
[745] | 472 | } |
---|
[105] | 473 | }; |
---|
| 474 | |
---|
[805] | 475 | std::string Scantable::formatDirection(const MDirection& md) const |
---|
[281] | 476 | { |
---|
| 477 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
| 478 | Int prec = 7; |
---|
| 479 | |
---|
[2575] | 480 | String ref = md.getRefString(); |
---|
[281] | 481 | MVAngle mvLon(t[0]); |
---|
| 482 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
[987] | 483 | uInt tp = md.getRef().getType(); |
---|
| 484 | if (tp == MDirection::GALACTIC || |
---|
| 485 | tp == MDirection::SUPERGAL ) { |
---|
| 486 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
| 487 | } |
---|
[281] | 488 | MVAngle mvLat(t[1]); |
---|
| 489 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
[2575] | 490 | return ref + String(" ") + sLon + String(" ") + sLat; |
---|
[281] | 491 | } |
---|
| 492 | |
---|
| 493 | |
---|
[805] | 494 | std::string Scantable::getFluxUnit() const |
---|
[206] | 495 | { |
---|
[847] | 496 | return table_.keywordSet().asString("FluxUnit"); |
---|
[206] | 497 | } |
---|
| 498 | |
---|
[805] | 499 | void Scantable::setFluxUnit(const std::string& unit) |
---|
[218] | 500 | { |
---|
| 501 | String tmp(unit); |
---|
| 502 | Unit tU(tmp); |
---|
| 503 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
| 504 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
| 505 | } else { |
---|
| 506 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
| 507 | } |
---|
| 508 | } |
---|
| 509 | |
---|
[805] | 510 | void Scantable::setInstrument(const std::string& name) |
---|
[236] | 511 | { |
---|
[805] | 512 | bool throwIt = true; |
---|
[996] | 513 | // create an Instrument to see if this is valid |
---|
| 514 | STAttr::convertInstrument(name, throwIt); |
---|
[236] | 515 | String nameU(name); |
---|
| 516 | nameU.upcase(); |
---|
| 517 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
| 518 | } |
---|
| 519 | |
---|
[1189] | 520 | void Scantable::setFeedType(const std::string& feedtype) |
---|
| 521 | { |
---|
| 522 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
| 523 | std::string msg = "Illegal feed type "+ feedtype; |
---|
| 524 | throw(casa::AipsError(msg)); |
---|
| 525 | } |
---|
| 526 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
| 527 | } |
---|
| 528 | |
---|
[1743] | 529 | MPosition Scantable::getAntennaPosition() const |
---|
[805] | 530 | { |
---|
| 531 | Vector<Double> antpos; |
---|
| 532 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
| 533 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
| 534 | return MPosition(mvpos); |
---|
| 535 | } |
---|
[281] | 536 | |
---|
[805] | 537 | void Scantable::makePersistent(const std::string& filename) |
---|
| 538 | { |
---|
| 539 | String inname(filename); |
---|
| 540 | Path path(inname); |
---|
[1111] | 541 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
[805] | 542 | inname = path.expandedName(); |
---|
[2030] | 543 | // 2011/03/04 TN |
---|
| 544 | // We can comment out this workaround since the essential bug is |
---|
| 545 | // fixed in casacore (r20889 in google code). |
---|
| 546 | table_.deepCopy(inname, Table::New); |
---|
| 547 | // // WORKAROUND !!! for Table bug |
---|
| 548 | // // Remove when fixed in casacore |
---|
| 549 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
| 550 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
| 551 | // tab.deepCopy(inname, Table::New); |
---|
| 552 | // tab.markForDelete(); |
---|
| 553 | // |
---|
| 554 | // } else { |
---|
| 555 | // table_.deepCopy(inname, Table::New); |
---|
| 556 | // } |
---|
[805] | 557 | } |
---|
| 558 | |
---|
[837] | 559 | int Scantable::nbeam( int scanno ) const |
---|
[805] | 560 | { |
---|
| 561 | if ( scanno < 0 ) { |
---|
| 562 | Int n; |
---|
| 563 | table_.keywordSet().get("nBeam",n); |
---|
| 564 | return int(n); |
---|
[105] | 565 | } else { |
---|
[805] | 566 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 567 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 568 | ROTableRow row(t); |
---|
| 569 | const TableRecord& rec = row.get(0); |
---|
| 570 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 571 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 572 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 573 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
[805] | 574 | return int(v.nelements()); |
---|
[105] | 575 | } |
---|
[805] | 576 | return 0; |
---|
| 577 | } |
---|
[455] | 578 | |
---|
[837] | 579 | int Scantable::nif( int scanno ) const |
---|
[805] | 580 | { |
---|
| 581 | if ( scanno < 0 ) { |
---|
| 582 | Int n; |
---|
| 583 | table_.keywordSet().get("nIF",n); |
---|
| 584 | return int(n); |
---|
| 585 | } else { |
---|
| 586 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 587 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 588 | ROTableRow row(t); |
---|
| 589 | const TableRecord& rec = row.get(0); |
---|
| 590 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 591 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 592 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 593 | if ( subt.nrow() == 0 ) return 0; |
---|
| 594 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
[805] | 595 | return int(v.nelements()); |
---|
[2] | 596 | } |
---|
[805] | 597 | return 0; |
---|
| 598 | } |
---|
[321] | 599 | |
---|
[837] | 600 | int Scantable::npol( int scanno ) const |
---|
[805] | 601 | { |
---|
| 602 | if ( scanno < 0 ) { |
---|
| 603 | Int n; |
---|
| 604 | table_.keywordSet().get("nPol",n); |
---|
| 605 | return n; |
---|
| 606 | } else { |
---|
| 607 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 608 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 609 | ROTableRow row(t); |
---|
| 610 | const TableRecord& rec = row.get(0); |
---|
| 611 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 612 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 613 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 614 | if ( subt.nrow() == 0 ) return 0; |
---|
| 615 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
[805] | 616 | return int(v.nelements()); |
---|
[321] | 617 | } |
---|
[805] | 618 | return 0; |
---|
[2] | 619 | } |
---|
[805] | 620 | |
---|
[845] | 621 | int Scantable::ncycle( int scanno ) const |
---|
[206] | 622 | { |
---|
[805] | 623 | if ( scanno < 0 ) { |
---|
[837] | 624 | Block<String> cols(2); |
---|
| 625 | cols[0] = "SCANNO"; |
---|
| 626 | cols[1] = "CYCLENO"; |
---|
| 627 | TableIterator it(table_, cols); |
---|
| 628 | int n = 0; |
---|
| 629 | while ( !it.pastEnd() ) { |
---|
| 630 | ++n; |
---|
[902] | 631 | ++it; |
---|
[837] | 632 | } |
---|
| 633 | return n; |
---|
[805] | 634 | } else { |
---|
[888] | 635 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 636 | ROTableRow row(t); |
---|
| 637 | const TableRecord& rec = row.get(0); |
---|
| 638 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 639 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 640 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
| 641 | if ( subt.nrow() == 0 ) return 0; |
---|
| 642 | return int(subt.nrow()); |
---|
[805] | 643 | } |
---|
| 644 | return 0; |
---|
[18] | 645 | } |
---|
[455] | 646 | |
---|
| 647 | |
---|
[845] | 648 | int Scantable::nrow( int scanno ) const |
---|
[805] | 649 | { |
---|
[845] | 650 | return int(table_.nrow()); |
---|
| 651 | } |
---|
| 652 | |
---|
| 653 | int Scantable::nchan( int ifno ) const |
---|
| 654 | { |
---|
| 655 | if ( ifno < 0 ) { |
---|
[805] | 656 | Int n; |
---|
| 657 | table_.keywordSet().get("nChan",n); |
---|
| 658 | return int(n); |
---|
| 659 | } else { |
---|
[1360] | 660 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
| 661 | // vary with these |
---|
[2244] | 662 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
[888] | 663 | if ( t.nrow() == 0 ) return 0; |
---|
| 664 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
[923] | 665 | return v.shape(0)(0); |
---|
[805] | 666 | } |
---|
| 667 | return 0; |
---|
[18] | 668 | } |
---|
[455] | 669 | |
---|
[1111] | 670 | int Scantable::nscan() const { |
---|
| 671 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
[1148] | 672 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
[1111] | 673 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 674 | return int(nout); |
---|
| 675 | } |
---|
| 676 | |
---|
[923] | 677 | int Scantable::getChannels(int whichrow) const |
---|
| 678 | { |
---|
| 679 | return specCol_.shape(whichrow)(0); |
---|
| 680 | } |
---|
[847] | 681 | |
---|
| 682 | int Scantable::getBeam(int whichrow) const |
---|
| 683 | { |
---|
| 684 | return beamCol_(whichrow); |
---|
| 685 | } |
---|
| 686 | |
---|
[1694] | 687 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
[1111] | 688 | { |
---|
| 689 | Vector<uInt> nos(col.getColumn()); |
---|
[1148] | 690 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 691 | nos.resize(n, True); |
---|
[1111] | 692 | std::vector<uint> stlout; |
---|
| 693 | nos.tovector(stlout); |
---|
| 694 | return stlout; |
---|
| 695 | } |
---|
| 696 | |
---|
[847] | 697 | int Scantable::getIF(int whichrow) const |
---|
| 698 | { |
---|
| 699 | return ifCol_(whichrow); |
---|
| 700 | } |
---|
| 701 | |
---|
| 702 | int Scantable::getPol(int whichrow) const |
---|
| 703 | { |
---|
| 704 | return polCol_(whichrow); |
---|
| 705 | } |
---|
| 706 | |
---|
[805] | 707 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
| 708 | { |
---|
[1947] | 709 | return formatTime(me, showdate, 0); |
---|
| 710 | } |
---|
| 711 | |
---|
| 712 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
| 713 | { |
---|
[805] | 714 | MVTime mvt(me.getValue()); |
---|
| 715 | if (showdate) |
---|
[1947] | 716 | //mvt.setFormat(MVTime::YMD); |
---|
| 717 | mvt.setFormat(MVTime::YMD, prec); |
---|
[805] | 718 | else |
---|
[1947] | 719 | //mvt.setFormat(MVTime::TIME); |
---|
| 720 | mvt.setFormat(MVTime::TIME, prec); |
---|
[805] | 721 | ostringstream oss; |
---|
| 722 | oss << mvt; |
---|
| 723 | return String(oss); |
---|
| 724 | } |
---|
[488] | 725 | |
---|
[805] | 726 | void Scantable::calculateAZEL() |
---|
| 727 | { |
---|
| 728 | MPosition mp = getAntennaPosition(); |
---|
| 729 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 730 | ostringstream oss; |
---|
| 731 | oss << "Computed azimuth/elevation using " << endl |
---|
| 732 | << mp << endl; |
---|
[996] | 733 | for (Int i=0; i<nrow(); ++i) { |
---|
[805] | 734 | MEpoch me = timeCol(i); |
---|
[987] | 735 | MDirection md = getDirection(i); |
---|
[805] | 736 | oss << " Time: " << formatTime(me,False) << " Direction: " << formatDirection(md) |
---|
| 737 | << endl << " => "; |
---|
| 738 | MeasFrame frame(mp, me); |
---|
| 739 | Vector<Double> azel = |
---|
| 740 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
| 741 | frame) |
---|
| 742 | )().getAngle("rad").getValue(); |
---|
[923] | 743 | azCol_.put(i,Float(azel[0])); |
---|
| 744 | elCol_.put(i,Float(azel[1])); |
---|
[805] | 745 | oss << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
| 746 | << azel[1]/C::pi*180.0 << " (deg)" << endl; |
---|
[16] | 747 | } |
---|
[805] | 748 | pushLog(String(oss)); |
---|
| 749 | } |
---|
[89] | 750 | |
---|
[1819] | 751 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 752 | { |
---|
| 753 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
| 754 | Vector<uChar> flgs = flagsCol_(i); |
---|
| 755 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
| 756 | flagsCol_.put(i, flgs); |
---|
| 757 | } |
---|
| 758 | } |
---|
| 759 | |
---|
| 760 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 761 | { |
---|
| 762 | Vector<uChar> flags; |
---|
| 763 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 764 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
| 765 | Vector<Bool> bflag(flags.shape()); |
---|
| 766 | convertArray(bflag, flags); |
---|
| 767 | //bflag = !bflag; |
---|
| 768 | |
---|
| 769 | std::vector<bool> mask; |
---|
| 770 | bflag.tovector(mask); |
---|
| 771 | return mask; |
---|
| 772 | } |
---|
| 773 | |
---|
| 774 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
| 775 | Vector<uChar> flgs) |
---|
| 776 | { |
---|
| 777 | Vector<Float> spcs = specCol_(whichrow); |
---|
[2348] | 778 | uInt nchannel = spcs.nelements(); |
---|
[1819] | 779 | if (spcs.nelements() != nchannel) { |
---|
| 780 | throw(AipsError("Data has incorrect number of channels")); |
---|
| 781 | } |
---|
| 782 | uChar userflag = 1 << 7; |
---|
| 783 | if (unflag) { |
---|
| 784 | userflag = 0 << 7; |
---|
| 785 | } |
---|
| 786 | if (clipoutside) { |
---|
| 787 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 788 | Float spc = spcs(j); |
---|
| 789 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
| 790 | flgs(j) = userflag; |
---|
| 791 | } |
---|
| 792 | } |
---|
| 793 | } else { |
---|
| 794 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 795 | Float spc = spcs(j); |
---|
| 796 | if ((spc < uthres) && (spc > dthres)) { |
---|
| 797 | flgs(j) = userflag; |
---|
| 798 | } |
---|
| 799 | } |
---|
| 800 | } |
---|
| 801 | } |
---|
| 802 | |
---|
[1994] | 803 | |
---|
| 804 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
[1333] | 805 | std::vector<bool>::const_iterator it; |
---|
| 806 | uInt ntrue = 0; |
---|
[1994] | 807 | if (whichrow >= int(table_.nrow()) ) { |
---|
| 808 | throw(AipsError("Invalid row number")); |
---|
| 809 | } |
---|
[1333] | 810 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 811 | if ( *it ) { |
---|
| 812 | ntrue++; |
---|
| 813 | } |
---|
| 814 | } |
---|
[1994] | 815 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
| 816 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
[1000] | 817 | throw(AipsError("Trying to flag whole scantable.")); |
---|
[1994] | 818 | uChar userflag = 1 << 7; |
---|
| 819 | if ( unflag ) { |
---|
| 820 | userflag = 0 << 7; |
---|
| 821 | } |
---|
| 822 | if (whichrow > -1 ) { |
---|
| 823 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
| 824 | } else { |
---|
[1000] | 825 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
[1994] | 826 | applyChanFlag(i, msk, userflag); |
---|
[1000] | 827 | } |
---|
[1994] | 828 | } |
---|
| 829 | } |
---|
| 830 | |
---|
| 831 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
| 832 | { |
---|
| 833 | if (whichrow >= table_.nrow() ) { |
---|
| 834 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
| 835 | } |
---|
| 836 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
| 837 | if ( msk.size() == 0 ) { |
---|
| 838 | flgs = flagval; |
---|
| 839 | flagsCol_.put(whichrow, flgs); |
---|
[1000] | 840 | return; |
---|
| 841 | } |
---|
[2348] | 842 | if ( int(msk.size()) != nchan( getIF(whichrow) ) ) { |
---|
[1000] | 843 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
| 844 | } |
---|
[1994] | 845 | if ( flgs.nelements() != msk.size() ) { |
---|
| 846 | throw(AipsError("Mask has incorrect number of channels." |
---|
| 847 | " Probably varying with IF. Please flag per IF")); |
---|
| 848 | } |
---|
| 849 | std::vector<bool>::const_iterator it; |
---|
| 850 | uInt j = 0; |
---|
| 851 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 852 | if ( *it ) { |
---|
| 853 | flgs(j) = flagval; |
---|
[1000] | 854 | } |
---|
[1994] | 855 | ++j; |
---|
[1000] | 856 | } |
---|
[1994] | 857 | flagsCol_.put(whichrow, flgs); |
---|
[865] | 858 | } |
---|
| 859 | |
---|
[1819] | 860 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
| 861 | { |
---|
| 862 | if ( selector_.empty() && (rows.size() == table_.nrow()) ) |
---|
| 863 | throw(AipsError("Trying to flag whole scantable.")); |
---|
| 864 | |
---|
| 865 | uInt rowflag = (unflag ? 0 : 1); |
---|
| 866 | std::vector<uInt>::const_iterator it; |
---|
| 867 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
| 868 | flagrowCol_.put(*it, rowflag); |
---|
| 869 | } |
---|
| 870 | |
---|
[805] | 871 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
| 872 | { |
---|
| 873 | Vector<uChar> flags; |
---|
| 874 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 875 | Vector<Bool> bflag(flags.shape()); |
---|
| 876 | convertArray(bflag, flags); |
---|
| 877 | bflag = !bflag; |
---|
| 878 | std::vector<bool> mask; |
---|
| 879 | bflag.tovector(mask); |
---|
| 880 | return mask; |
---|
| 881 | } |
---|
[89] | 882 | |
---|
[896] | 883 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
[902] | 884 | const std::string& poltype ) const |
---|
[805] | 885 | { |
---|
[905] | 886 | String ptype = poltype; |
---|
| 887 | if (poltype == "" ) ptype = getPolType(); |
---|
[902] | 888 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
| 889 | throw(AipsError("Illegal row number.")); |
---|
[896] | 890 | std::vector<float> out; |
---|
[805] | 891 | Vector<Float> arr; |
---|
[896] | 892 | uInt requestedpol = polCol_(whichrow); |
---|
| 893 | String basetype = getPolType(); |
---|
[905] | 894 | if ( ptype == basetype ) { |
---|
[896] | 895 | specCol_.get(whichrow, arr); |
---|
| 896 | } else { |
---|
[1598] | 897 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
[1586] | 898 | basetype)); |
---|
[1334] | 899 | uInt row = uInt(whichrow); |
---|
| 900 | stpol->setSpectra(getPolMatrix(row)); |
---|
[2047] | 901 | Float fang,fhand; |
---|
[1586] | 902 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
[1334] | 903 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
[1586] | 904 | stpol->setPhaseCorrections(fang, fhand); |
---|
[1334] | 905 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
[896] | 906 | } |
---|
[902] | 907 | if ( arr.nelements() == 0 ) |
---|
| 908 | pushLog("Not enough polarisations present to do the conversion."); |
---|
[805] | 909 | arr.tovector(out); |
---|
| 910 | return out; |
---|
[89] | 911 | } |
---|
[212] | 912 | |
---|
[1360] | 913 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
[884] | 914 | int whichrow ) |
---|
| 915 | { |
---|
| 916 | Vector<Float> spectrum(spec); |
---|
| 917 | Vector<Float> arr; |
---|
| 918 | specCol_.get(whichrow, arr); |
---|
| 919 | if ( spectrum.nelements() != arr.nelements() ) |
---|
[896] | 920 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
[884] | 921 | specCol_.put(whichrow, spectrum); |
---|
| 922 | } |
---|
| 923 | |
---|
| 924 | |
---|
[805] | 925 | String Scantable::generateName() |
---|
[745] | 926 | { |
---|
[805] | 927 | return (File::newUniqueName("./","temp")).baseName(); |
---|
[212] | 928 | } |
---|
| 929 | |
---|
[805] | 930 | const casa::Table& Scantable::table( ) const |
---|
[212] | 931 | { |
---|
[805] | 932 | return table_; |
---|
[212] | 933 | } |
---|
| 934 | |
---|
[805] | 935 | casa::Table& Scantable::table( ) |
---|
[386] | 936 | { |
---|
[805] | 937 | return table_; |
---|
[386] | 938 | } |
---|
| 939 | |
---|
[896] | 940 | std::string Scantable::getPolType() const |
---|
| 941 | { |
---|
| 942 | return table_.keywordSet().asString("POLTYPE"); |
---|
| 943 | } |
---|
| 944 | |
---|
[805] | 945 | void Scantable::unsetSelection() |
---|
[380] | 946 | { |
---|
[805] | 947 | table_ = originalTable_; |
---|
[847] | 948 | attach(); |
---|
[805] | 949 | selector_.reset(); |
---|
[380] | 950 | } |
---|
[386] | 951 | |
---|
[805] | 952 | void Scantable::setSelection( const STSelector& selection ) |
---|
[430] | 953 | { |
---|
[805] | 954 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
| 955 | if ( tab.nrow() == 0 ) { |
---|
| 956 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
| 957 | } |
---|
| 958 | table_ = tab; |
---|
[847] | 959 | attach(); |
---|
[2084] | 960 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
| 961 | // vector<uint> selectedIFs = getIFNos() ; |
---|
| 962 | // Int newnIF = selectedIFs.size() ; |
---|
| 963 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
| 964 | // if ( newnIF != 0 ) { |
---|
| 965 | // Int newnChan = 0 ; |
---|
| 966 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
| 967 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
| 968 | // if ( newnChan > nChan ) |
---|
| 969 | // newnChan = nChan ; |
---|
| 970 | // } |
---|
| 971 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
| 972 | // } |
---|
| 973 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
[805] | 974 | selector_ = selection; |
---|
[430] | 975 | } |
---|
| 976 | |
---|
[2111] | 977 | |
---|
[2163] | 978 | std::string Scantable::headerSummary() |
---|
[447] | 979 | { |
---|
[805] | 980 | // Format header info |
---|
[2111] | 981 | // STHeader sdh; |
---|
| 982 | // sdh = getHeader(); |
---|
| 983 | // sdh.print(); |
---|
[805] | 984 | ostringstream oss; |
---|
| 985 | oss.flags(std::ios_base::left); |
---|
[2290] | 986 | String tmp; |
---|
| 987 | // Project |
---|
| 988 | table_.keywordSet().get("Project", tmp); |
---|
| 989 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 990 | // Observation date |
---|
| 991 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 992 | // Observer |
---|
| 993 | oss << setw(15) << "Observer:" |
---|
| 994 | << table_.keywordSet().asString("Observer") << endl; |
---|
| 995 | // Antenna Name |
---|
| 996 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 997 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 998 | // Obs type |
---|
| 999 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1000 | // Records (nrow) |
---|
| 1001 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
| 1002 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1003 | // Beams, IFs, Polarizations, and Channels |
---|
[805] | 1004 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1005 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
[896] | 1006 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1007 | << "(" << getPolType() << ")" << endl |
---|
[1694] | 1008 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[2290] | 1009 | // Flux unit |
---|
| 1010 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1011 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
| 1012 | // Abscissa Unit |
---|
| 1013 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
| 1014 | // Selection |
---|
| 1015 | oss << selector_.print() << endl; |
---|
| 1016 | |
---|
| 1017 | return String(oss); |
---|
| 1018 | } |
---|
| 1019 | |
---|
| 1020 | void Scantable::summary( const std::string& filename ) |
---|
| 1021 | { |
---|
| 1022 | ostringstream oss; |
---|
| 1023 | ofstream ofs; |
---|
| 1024 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1025 | |
---|
| 1026 | if (filename != "") |
---|
| 1027 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1028 | |
---|
| 1029 | oss << endl; |
---|
| 1030 | oss << asap::SEPERATOR << endl; |
---|
| 1031 | oss << " Scan Table Summary" << endl; |
---|
| 1032 | oss << asap::SEPERATOR << endl; |
---|
| 1033 | |
---|
| 1034 | // Format header info |
---|
| 1035 | oss << headerSummary(); |
---|
| 1036 | oss << endl; |
---|
| 1037 | |
---|
| 1038 | if (table_.nrow() <= 0){ |
---|
| 1039 | oss << asap::SEPERATOR << endl; |
---|
| 1040 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
| 1041 | oss << asap::SEPERATOR << endl; |
---|
| 1042 | |
---|
| 1043 | ols << String(oss) << LogIO::POST; |
---|
| 1044 | if (ofs) { |
---|
| 1045 | ofs << String(oss) << flush; |
---|
| 1046 | ofs.close(); |
---|
| 1047 | } |
---|
| 1048 | return; |
---|
| 1049 | } |
---|
| 1050 | |
---|
| 1051 | |
---|
| 1052 | |
---|
| 1053 | // main table |
---|
| 1054 | String dirtype = "Position (" |
---|
| 1055 | + getDirectionRefString() |
---|
| 1056 | + ")"; |
---|
| 1057 | oss.flags(std::ios_base::left); |
---|
| 1058 | oss << setw(5) << "Scan" |
---|
| 1059 | << setw(15) << "Source" |
---|
| 1060 | << setw(35) << "Time range" |
---|
| 1061 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
| 1062 | << setw(7) << "Record" |
---|
| 1063 | << setw(8) << "SrcType" |
---|
| 1064 | << setw(8) << "FreqIDs" |
---|
| 1065 | << setw(7) << "MolIDs" << endl; |
---|
| 1066 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
| 1067 | << setw(23) << dirtype << endl; |
---|
| 1068 | |
---|
| 1069 | oss << asap::SEPERATOR << endl; |
---|
| 1070 | |
---|
| 1071 | // Flush summary and clear up the string |
---|
| 1072 | ols << String(oss) << LogIO::POST; |
---|
| 1073 | if (ofs) ofs << String(oss) << flush; |
---|
| 1074 | oss.str(""); |
---|
| 1075 | oss.clear(); |
---|
| 1076 | |
---|
| 1077 | |
---|
| 1078 | // Get Freq_ID map |
---|
| 1079 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
| 1080 | Int nfid = ftabIds.nrow(); |
---|
| 1081 | if (nfid <= 0){ |
---|
| 1082 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
| 1083 | oss << asap::SEPERATOR << endl; |
---|
| 1084 | |
---|
| 1085 | ols << String(oss) << LogIO::POST; |
---|
| 1086 | if (ofs) { |
---|
| 1087 | ofs << String(oss) << flush; |
---|
| 1088 | ofs.close(); |
---|
| 1089 | } |
---|
| 1090 | return; |
---|
| 1091 | } |
---|
| 1092 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
| 1093 | // the orders are identical to ID in FREQ subtable |
---|
| 1094 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
| 1095 | Vector<Int> fIdchans(nfid,-1); |
---|
| 1096 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
| 1097 | for (Int i=0; i < nfid; i++){ |
---|
| 1098 | // fidMap[freqId] returns row number in FREQ subtable |
---|
| 1099 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
| 1100 | ifNos[i] = Vector<uInt>(); |
---|
| 1101 | polNos[i] = Vector<uInt>(); |
---|
| 1102 | } |
---|
| 1103 | |
---|
| 1104 | TableIterator iter(table_, "SCANNO"); |
---|
| 1105 | |
---|
| 1106 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
| 1107 | Vector<uInt> freqids; |
---|
| 1108 | Vector<uInt> molids; |
---|
| 1109 | Vector<uInt> beamids(1,0); |
---|
| 1110 | Vector<MDirection> beamDirs; |
---|
| 1111 | Vector<Int> stypeids(1,0); |
---|
| 1112 | Vector<String> stypestrs; |
---|
| 1113 | Int nfreq(1); |
---|
| 1114 | Int nmol(1); |
---|
| 1115 | uInt nbeam(1); |
---|
| 1116 | uInt nstype(1); |
---|
| 1117 | |
---|
| 1118 | Double btime(0.0), etime(0.0); |
---|
| 1119 | Double meanIntTim(0.0); |
---|
| 1120 | |
---|
| 1121 | uInt currFreqId(0), ftabRow(0); |
---|
| 1122 | Int iflen(0), pollen(0); |
---|
| 1123 | |
---|
| 1124 | while (!iter.pastEnd()) { |
---|
| 1125 | Table subt = iter.table(); |
---|
| 1126 | uInt snrow = subt.nrow(); |
---|
| 1127 | ROTableRow row(subt); |
---|
| 1128 | const TableRecord& rec = row.get(0); |
---|
| 1129 | |
---|
| 1130 | // relevant columns |
---|
| 1131 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
| 1132 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
| 1133 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
| 1134 | |
---|
| 1135 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
| 1136 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
| 1137 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
| 1138 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
| 1139 | |
---|
| 1140 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
| 1141 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
| 1142 | |
---|
| 1143 | |
---|
| 1144 | // Times |
---|
| 1145 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
| 1146 | minMax(btime, etime, mjdCol.getColumn()); |
---|
| 1147 | etime += meanIntTim/C::day; |
---|
| 1148 | |
---|
| 1149 | // MOLECULE_ID and FREQ_ID |
---|
| 1150 | molids = getNumbers(molIdCol); |
---|
| 1151 | molids.shape(nmol); |
---|
| 1152 | |
---|
| 1153 | freqids = getNumbers(freqIdCol); |
---|
| 1154 | freqids.shape(nfreq); |
---|
| 1155 | |
---|
| 1156 | // Add first beamid, and srcNames |
---|
| 1157 | beamids.resize(1,False); |
---|
| 1158 | beamDirs.resize(1,False); |
---|
| 1159 | beamids(0)=beamCol(0); |
---|
| 1160 | beamDirs(0)=dirCol(0); |
---|
| 1161 | nbeam = 1; |
---|
| 1162 | |
---|
| 1163 | stypeids.resize(1,False); |
---|
| 1164 | stypeids(0)=stypeCol(0); |
---|
| 1165 | nstype = 1; |
---|
| 1166 | |
---|
| 1167 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1168 | currFreqId=freqIdCol(0); |
---|
| 1169 | ftabRow = fidMap[currFreqId]; |
---|
| 1170 | // Assumes an identical number of channels per FREQ_ID |
---|
| 1171 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1172 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1173 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
| 1174 | } |
---|
| 1175 | // Should keep ifNos and polNos form the previous SCANNO |
---|
| 1176 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
| 1177 | ifNos[ftabRow].shape(iflen); |
---|
| 1178 | iflen++; |
---|
| 1179 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1180 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
| 1181 | } |
---|
| 1182 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
| 1183 | polNos[ftabRow].shape(pollen); |
---|
| 1184 | pollen++; |
---|
| 1185 | polNos[ftabRow].resize(pollen,True); |
---|
| 1186 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
| 1187 | } |
---|
| 1188 | |
---|
| 1189 | for (uInt i=1; i < snrow; i++){ |
---|
| 1190 | // Need to list BEAMNO and DIRECTION in the same order |
---|
| 1191 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
| 1192 | nbeam++; |
---|
| 1193 | beamids.resize(nbeam,True); |
---|
| 1194 | beamids(nbeam-1)=beamCol(i); |
---|
| 1195 | beamDirs.resize(nbeam,True); |
---|
| 1196 | beamDirs(nbeam-1)=dirCol(i); |
---|
| 1197 | } |
---|
| 1198 | |
---|
| 1199 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
| 1200 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
| 1201 | nstype++; |
---|
| 1202 | stypeids.resize(nstype,True); |
---|
| 1203 | stypeids(nstype-1)=stypeCol(i); |
---|
| 1204 | } |
---|
| 1205 | |
---|
| 1206 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1207 | currFreqId=freqIdCol(i); |
---|
| 1208 | ftabRow = fidMap[currFreqId]; |
---|
| 1209 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1210 | const TableRecord& rec = row.get(i); |
---|
| 1211 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1212 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
| 1213 | } |
---|
| 1214 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
| 1215 | ifNos[ftabRow].shape(iflen); |
---|
| 1216 | iflen++; |
---|
| 1217 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1218 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
| 1219 | } |
---|
| 1220 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
| 1221 | polNos[ftabRow].shape(pollen); |
---|
| 1222 | pollen++; |
---|
| 1223 | polNos[ftabRow].resize(pollen,True); |
---|
| 1224 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
| 1225 | } |
---|
| 1226 | } // end of row iteration |
---|
| 1227 | |
---|
| 1228 | stypestrs.resize(nstype,False); |
---|
| 1229 | for (uInt j=0; j < nstype; j++) |
---|
| 1230 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
| 1231 | |
---|
| 1232 | // Format Scan summary |
---|
| 1233 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1234 | << std::left << setw(1) << "" |
---|
| 1235 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1236 | << setw(21) << MVTime(btime).string(MVTime::YMD,7) |
---|
| 1237 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7) |
---|
| 1238 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
| 1239 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
| 1240 | << std::left << stypestrs << setw(1) << "" |
---|
| 1241 | << freqids << setw(1) << "" |
---|
| 1242 | << molids << endl; |
---|
| 1243 | // Format Beam summary |
---|
| 1244 | for (uInt j=0; j < nbeam; j++) { |
---|
| 1245 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
| 1246 | << formatDirection(beamDirs(j)) << endl; |
---|
| 1247 | } |
---|
| 1248 | // Flush summary every scan and clear up the string |
---|
| 1249 | ols << String(oss) << LogIO::POST; |
---|
| 1250 | if (ofs) ofs << String(oss) << flush; |
---|
| 1251 | oss.str(""); |
---|
| 1252 | oss.clear(); |
---|
| 1253 | |
---|
| 1254 | ++iter; |
---|
| 1255 | } // end of scan iteration |
---|
| 1256 | oss << asap::SEPERATOR << endl; |
---|
| 1257 | |
---|
| 1258 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
| 1259 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
| 1260 | oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
| 1261 | << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
| 1262 | << setw(8) << "Frame" |
---|
| 1263 | << setw(16) << "RefVal" |
---|
| 1264 | << setw(7) << "RefPix" |
---|
| 1265 | << setw(15) << "Increment" |
---|
| 1266 | << setw(9) << "Channels" |
---|
| 1267 | << setw(6) << "POLNOs" << endl; |
---|
| 1268 | Int tmplen; |
---|
| 1269 | for (Int i=0; i < nfid; i++){ |
---|
| 1270 | // List row=i of FREQUENCIES subtable |
---|
| 1271 | ifNos[i].shape(tmplen); |
---|
[2531] | 1272 | if (tmplen >= 1) { |
---|
[2290] | 1273 | oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
| 1274 | << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
| 1275 | << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
| 1276 | << setw(2) << "" |
---|
| 1277 | << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
[2531] | 1278 | << std::left << polNos[i]; |
---|
| 1279 | if (tmplen > 1) { |
---|
| 1280 | oss << " (" << tmplen << " chains)"; |
---|
| 1281 | } |
---|
| 1282 | oss << endl; |
---|
[2290] | 1283 | } |
---|
[2531] | 1284 | |
---|
[2290] | 1285 | } |
---|
| 1286 | oss << asap::SEPERATOR << endl; |
---|
| 1287 | |
---|
| 1288 | // List MOLECULES Table (currently lists all rows) |
---|
| 1289 | oss << "MOLECULES: " << endl; |
---|
| 1290 | if (molecules().nrow() <= 0) { |
---|
| 1291 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
| 1292 | } else { |
---|
| 1293 | ROTableRow row(molecules().table()); |
---|
| 1294 | oss << std::right << setw(5) << "ID" |
---|
| 1295 | << std::left << setw(3) << "" |
---|
| 1296 | << setw(18) << "RestFreq" |
---|
| 1297 | << setw(15) << "Name" << endl; |
---|
| 1298 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
| 1299 | const TableRecord& rec=row.get(i); |
---|
| 1300 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
| 1301 | << std::left << setw(3) << "" |
---|
| 1302 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
| 1303 | << rec.asArrayString("NAME") << endl; |
---|
| 1304 | } |
---|
| 1305 | } |
---|
| 1306 | oss << asap::SEPERATOR << endl; |
---|
| 1307 | ols << String(oss) << LogIO::POST; |
---|
| 1308 | if (ofs) { |
---|
| 1309 | ofs << String(oss) << flush; |
---|
| 1310 | ofs.close(); |
---|
| 1311 | } |
---|
| 1312 | // return String(oss); |
---|
| 1313 | } |
---|
| 1314 | |
---|
| 1315 | |
---|
| 1316 | std::string Scantable::oldheaderSummary() |
---|
| 1317 | { |
---|
| 1318 | // Format header info |
---|
| 1319 | // STHeader sdh; |
---|
| 1320 | // sdh = getHeader(); |
---|
| 1321 | // sdh.print(); |
---|
| 1322 | ostringstream oss; |
---|
| 1323 | oss.flags(std::ios_base::left); |
---|
| 1324 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1325 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
| 1326 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1327 | << "(" << getPolType() << ")" << endl |
---|
| 1328 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[805] | 1329 | String tmp; |
---|
[860] | 1330 | oss << setw(15) << "Observer:" |
---|
| 1331 | << table_.keywordSet().asString("Observer") << endl; |
---|
[805] | 1332 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1333 | table_.keywordSet().get("Project", tmp); |
---|
| 1334 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1335 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1336 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1337 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1338 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1339 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1340 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
[1819] | 1341 | int nid = moleculeTable_.nrow(); |
---|
| 1342 | Bool firstline = True; |
---|
[805] | 1343 | oss << setw(15) << "Rest Freqs:"; |
---|
[1819] | 1344 | for (int i=0; i<nid; i++) { |
---|
[2244] | 1345 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
[1819] | 1346 | if (t.nrow() > 0) { |
---|
| 1347 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
| 1348 | if (vec.nelements() > 0) { |
---|
| 1349 | if (firstline) { |
---|
| 1350 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1351 | firstline=False; |
---|
| 1352 | } |
---|
| 1353 | else{ |
---|
| 1354 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1355 | } |
---|
| 1356 | } else { |
---|
| 1357 | oss << "none" << endl; |
---|
| 1358 | } |
---|
| 1359 | } |
---|
[805] | 1360 | } |
---|
[941] | 1361 | |
---|
| 1362 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
[805] | 1363 | oss << selector_.print() << endl; |
---|
[2111] | 1364 | return String(oss); |
---|
| 1365 | } |
---|
| 1366 | |
---|
[2286] | 1367 | //std::string Scantable::summary( const std::string& filename ) |
---|
[2290] | 1368 | void Scantable::oldsummary( const std::string& filename ) |
---|
[2111] | 1369 | { |
---|
| 1370 | ostringstream oss; |
---|
[2286] | 1371 | ofstream ofs; |
---|
| 1372 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1373 | |
---|
| 1374 | if (filename != "") |
---|
| 1375 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1376 | |
---|
[805] | 1377 | oss << endl; |
---|
[2111] | 1378 | oss << asap::SEPERATOR << endl; |
---|
| 1379 | oss << " Scan Table Summary" << endl; |
---|
| 1380 | oss << asap::SEPERATOR << endl; |
---|
| 1381 | |
---|
| 1382 | // Format header info |
---|
[2290] | 1383 | oss << oldheaderSummary(); |
---|
[2111] | 1384 | oss << endl; |
---|
| 1385 | |
---|
[805] | 1386 | // main table |
---|
| 1387 | String dirtype = "Position (" |
---|
[987] | 1388 | + getDirectionRefString() |
---|
[805] | 1389 | + ")"; |
---|
[2111] | 1390 | oss.flags(std::ios_base::left); |
---|
[941] | 1391 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
[2005] | 1392 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
| 1393 | << setw(15) << "Source Type" << endl; |
---|
[941] | 1394 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
[1694] | 1395 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
[805] | 1396 | << setw(8) << "Frame" << setw(16) |
---|
[1694] | 1397 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
| 1398 | << setw(7) << "Channels" |
---|
| 1399 | << endl; |
---|
[805] | 1400 | oss << asap::SEPERATOR << endl; |
---|
[2286] | 1401 | |
---|
| 1402 | // Flush summary and clear up the string |
---|
| 1403 | ols << String(oss) << LogIO::POST; |
---|
| 1404 | if (ofs) ofs << String(oss) << flush; |
---|
| 1405 | oss.str(""); |
---|
| 1406 | oss.clear(); |
---|
| 1407 | |
---|
[805] | 1408 | TableIterator iter(table_, "SCANNO"); |
---|
| 1409 | while (!iter.pastEnd()) { |
---|
| 1410 | Table subt = iter.table(); |
---|
| 1411 | ROTableRow row(subt); |
---|
| 1412 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
| 1413 | const TableRecord& rec = row.get(0); |
---|
| 1414 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1415 | << std::left << setw(1) << "" |
---|
| 1416 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1417 | << setw(10) << formatTime(timeCol(0), false); |
---|
| 1418 | // count the cycles in the scan |
---|
| 1419 | TableIterator cyciter(subt, "CYCLENO"); |
---|
| 1420 | int nint = 0; |
---|
| 1421 | while (!cyciter.pastEnd()) { |
---|
| 1422 | ++nint; |
---|
| 1423 | ++cyciter; |
---|
| 1424 | } |
---|
| 1425 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
[2005] | 1426 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
| 1427 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
[447] | 1428 | |
---|
[805] | 1429 | TableIterator biter(subt, "BEAMNO"); |
---|
| 1430 | while (!biter.pastEnd()) { |
---|
| 1431 | Table bsubt = biter.table(); |
---|
| 1432 | ROTableRow brow(bsubt); |
---|
| 1433 | const TableRecord& brec = brow.get(0); |
---|
[1000] | 1434 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
[941] | 1435 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
[987] | 1436 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
[805] | 1437 | TableIterator iiter(bsubt, "IFNO"); |
---|
| 1438 | while (!iiter.pastEnd()) { |
---|
| 1439 | Table isubt = iiter.table(); |
---|
| 1440 | ROTableRow irow(isubt); |
---|
| 1441 | const TableRecord& irec = irow.get(0); |
---|
[1694] | 1442 | oss << setw(9) << ""; |
---|
[941] | 1443 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
[1694] | 1444 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
| 1445 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
[1375] | 1446 | << endl; |
---|
[447] | 1447 | |
---|
[805] | 1448 | ++iiter; |
---|
| 1449 | } |
---|
| 1450 | ++biter; |
---|
| 1451 | } |
---|
[2286] | 1452 | // Flush summary every scan and clear up the string |
---|
| 1453 | ols << String(oss) << LogIO::POST; |
---|
| 1454 | if (ofs) ofs << String(oss) << flush; |
---|
| 1455 | oss.str(""); |
---|
| 1456 | oss.clear(); |
---|
| 1457 | |
---|
[805] | 1458 | ++iter; |
---|
[447] | 1459 | } |
---|
[2286] | 1460 | oss << asap::SEPERATOR << endl; |
---|
| 1461 | ols << String(oss) << LogIO::POST; |
---|
| 1462 | if (ofs) { |
---|
[2290] | 1463 | ofs << String(oss) << flush; |
---|
[2286] | 1464 | ofs.close(); |
---|
| 1465 | } |
---|
| 1466 | // return String(oss); |
---|
[447] | 1467 | } |
---|
| 1468 | |
---|
[1947] | 1469 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
| 1470 | // { |
---|
| 1471 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 1472 | // MEpoch me; |
---|
| 1473 | // if (whichrow > -1) { |
---|
| 1474 | // me = timeCol(uInt(whichrow)); |
---|
| 1475 | // } else { |
---|
| 1476 | // Double tm; |
---|
| 1477 | // table_.keywordSet().get("UTC",tm); |
---|
| 1478 | // me = MEpoch(MVEpoch(tm)); |
---|
| 1479 | // } |
---|
| 1480 | // return formatTime(me, showdate); |
---|
| 1481 | // } |
---|
| 1482 | |
---|
| 1483 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
[777] | 1484 | { |
---|
[805] | 1485 | MEpoch me; |
---|
[1947] | 1486 | me = getEpoch(whichrow); |
---|
| 1487 | return formatTime(me, showdate, prec); |
---|
[777] | 1488 | } |
---|
[805] | 1489 | |
---|
[1411] | 1490 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
| 1491 | { |
---|
| 1492 | if (whichrow > -1) { |
---|
| 1493 | return timeCol_(uInt(whichrow)); |
---|
| 1494 | } else { |
---|
| 1495 | Double tm; |
---|
| 1496 | table_.keywordSet().get("UTC",tm); |
---|
[1598] | 1497 | return MEpoch(MVEpoch(tm)); |
---|
[1411] | 1498 | } |
---|
| 1499 | } |
---|
| 1500 | |
---|
[1068] | 1501 | std::string Scantable::getDirectionString(int whichrow) const |
---|
| 1502 | { |
---|
| 1503 | return formatDirection(getDirection(uInt(whichrow))); |
---|
| 1504 | } |
---|
| 1505 | |
---|
[1598] | 1506 | |
---|
| 1507 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
| 1508 | const MPosition& mp = getAntennaPosition(); |
---|
| 1509 | const MDirection& md = getDirection(whichrow); |
---|
| 1510 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1511 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
| 1512 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[2346] | 1513 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
[1598] | 1514 | mfreqidCol_(whichrow)); |
---|
| 1515 | } |
---|
| 1516 | |
---|
[1360] | 1517 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
[865] | 1518 | { |
---|
[1507] | 1519 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
[865] | 1520 | std::vector<double> stlout; |
---|
| 1521 | int nchan = specCol_(whichrow).nelements(); |
---|
[2346] | 1522 | String us = freqTable_.getUnitString(); |
---|
[865] | 1523 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
| 1524 | for (int i=0; i<nchan; ++i) { |
---|
| 1525 | stlout.push_back(double(i)); |
---|
| 1526 | } |
---|
| 1527 | return stlout; |
---|
| 1528 | } |
---|
[1598] | 1529 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
[865] | 1530 | Vector<Double> pixel(nchan); |
---|
| 1531 | Vector<Double> world; |
---|
| 1532 | indgen(pixel); |
---|
| 1533 | if ( Unit(us) == Unit("Hz") ) { |
---|
| 1534 | for ( int i=0; i < nchan; ++i) { |
---|
| 1535 | Double world; |
---|
| 1536 | spc.toWorld(world, pixel[i]); |
---|
| 1537 | stlout.push_back(double(world)); |
---|
| 1538 | } |
---|
| 1539 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
| 1540 | Vector<Double> world; |
---|
| 1541 | spc.pixelToVelocity(world, pixel); |
---|
| 1542 | world.tovector(stlout); |
---|
| 1543 | } |
---|
| 1544 | return stlout; |
---|
| 1545 | } |
---|
[1360] | 1546 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
[987] | 1547 | { |
---|
| 1548 | MDirection::Types mdt; |
---|
| 1549 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
| 1550 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1551 | } |
---|
| 1552 | if ( refstr == "" ) { |
---|
| 1553 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1554 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
| 1555 | } else { |
---|
| 1556 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
| 1557 | } |
---|
| 1558 | } |
---|
[865] | 1559 | |
---|
[1360] | 1560 | std::string Scantable::getDirectionRefString( ) const |
---|
[987] | 1561 | { |
---|
| 1562 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1563 | } |
---|
| 1564 | |
---|
| 1565 | MDirection Scantable::getDirection(int whichrow ) const |
---|
| 1566 | { |
---|
| 1567 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1568 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1569 | if ( usertype != type ) { |
---|
| 1570 | MDirection::Types mdt; |
---|
| 1571 | if (!MDirection::getType(mdt, usertype)) { |
---|
| 1572 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1573 | } |
---|
| 1574 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
| 1575 | } else { |
---|
| 1576 | return dirCol_(uInt(whichrow)); |
---|
| 1577 | } |
---|
| 1578 | } |
---|
| 1579 | |
---|
[847] | 1580 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
| 1581 | { |
---|
[996] | 1582 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
[847] | 1583 | const MPosition& mp = getAntennaPosition(); |
---|
[987] | 1584 | const MDirection& md = getDirection(whichrow); |
---|
[847] | 1585 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1586 | //const Double& rf = mmolidCol_(whichrow); |
---|
| 1587 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[847] | 1588 | SpectralCoordinate spc = |
---|
[2346] | 1589 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
[847] | 1590 | |
---|
| 1591 | String s = "Channel"; |
---|
[2346] | 1592 | Unit u = Unit(freqTable_.getUnitString()); |
---|
[847] | 1593 | if (u == Unit("km/s")) { |
---|
[1170] | 1594 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
[847] | 1595 | } else if (u == Unit("Hz")) { |
---|
| 1596 | Vector<String> wau(1);wau = u.getName(); |
---|
| 1597 | spc.setWorldAxisUnits(wau); |
---|
[1170] | 1598 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
[847] | 1599 | } |
---|
| 1600 | return s; |
---|
| 1601 | |
---|
| 1602 | } |
---|
| 1603 | |
---|
[1819] | 1604 | /** |
---|
| 1605 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
[1170] | 1606 | const std::string& unit ) |
---|
[1819] | 1607 | **/ |
---|
| 1608 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
| 1609 | const std::string& unit ) |
---|
| 1610 | |
---|
[847] | 1611 | { |
---|
[923] | 1612 | ///@todo lookup in line table to fill in name and formattedname |
---|
[847] | 1613 | Unit u(unit); |
---|
[1819] | 1614 | //Quantum<Double> urf(rf, u); |
---|
| 1615 | Quantum<Vector<Double> >urf(rf, u); |
---|
| 1616 | Vector<String> formattedname(0); |
---|
| 1617 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
| 1618 | |
---|
| 1619 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
| 1620 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
[847] | 1621 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
| 1622 | tabvec = id; |
---|
| 1623 | } |
---|
| 1624 | |
---|
[1819] | 1625 | /** |
---|
| 1626 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
[847] | 1627 | { |
---|
| 1628 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
| 1629 | ///@todo implement |
---|
| 1630 | } |
---|
[1819] | 1631 | **/ |
---|
[2012] | 1632 | |
---|
[1819] | 1633 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
| 1634 | { |
---|
[2163] | 1635 | (void) name; // suppress unused warning |
---|
[1819] | 1636 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
| 1637 | ///@todo implement |
---|
| 1638 | } |
---|
[847] | 1639 | |
---|
[1360] | 1640 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
[852] | 1641 | { |
---|
| 1642 | std::vector<unsigned int> stlout; |
---|
| 1643 | Vector<uInt> vec = table_.rowNumbers(); |
---|
| 1644 | vec.tovector(stlout); |
---|
| 1645 | return stlout; |
---|
| 1646 | } |
---|
| 1647 | |
---|
[865] | 1648 | |
---|
[1360] | 1649 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
[896] | 1650 | { |
---|
| 1651 | ROTableRow row(table_); |
---|
| 1652 | const TableRecord& rec = row.get(whichrow); |
---|
| 1653 | Table t = |
---|
| 1654 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
| 1655 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 1656 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 1657 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 1658 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 1659 | return speccol.getColumn(); |
---|
| 1660 | } |
---|
[865] | 1661 | |
---|
[1360] | 1662 | std::vector< std::string > Scantable::columnNames( ) const |
---|
[902] | 1663 | { |
---|
| 1664 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
| 1665 | return mathutil::tovectorstring(vec); |
---|
| 1666 | } |
---|
[896] | 1667 | |
---|
[1360] | 1668 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
[915] | 1669 | { |
---|
| 1670 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
[972] | 1671 | } |
---|
[915] | 1672 | |
---|
[1360] | 1673 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
[972] | 1674 | { |
---|
[1819] | 1675 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
| 1676 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
| 1677 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
[972] | 1678 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
| 1679 | mfitidCol_.put(uInt(row), id); |
---|
| 1680 | } |
---|
[915] | 1681 | |
---|
[1360] | 1682 | void Scantable::shift(int npix) |
---|
| 1683 | { |
---|
| 1684 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
| 1685 | genSort( fids, Sort::Ascending, |
---|
| 1686 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 1687 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
[1567] | 1688 | frequencies().shiftRefPix(npix, fids[i]); |
---|
[1360] | 1689 | } |
---|
| 1690 | } |
---|
[987] | 1691 | |
---|
[1819] | 1692 | String Scantable::getAntennaName() const |
---|
[1391] | 1693 | { |
---|
| 1694 | String out; |
---|
| 1695 | table_.keywordSet().get("AntennaName", out); |
---|
[1987] | 1696 | String::size_type pos1 = out.find("@") ; |
---|
| 1697 | String::size_type pos2 = out.find("//") ; |
---|
| 1698 | if ( pos2 != String::npos ) |
---|
[2036] | 1699 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
[1987] | 1700 | else if ( pos1 != String::npos ) |
---|
| 1701 | out = out.substr(0,pos1) ; |
---|
[1391] | 1702 | return out; |
---|
[987] | 1703 | } |
---|
[1391] | 1704 | |
---|
[1730] | 1705 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
[1391] | 1706 | { |
---|
| 1707 | String tbpath; |
---|
| 1708 | int ret = 0; |
---|
| 1709 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
| 1710 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
| 1711 | Table t(tbpath,Table::Old); |
---|
| 1712 | // check each scan if other scan of the pair exist |
---|
| 1713 | int nscan = scanlist.size(); |
---|
| 1714 | for (int i = 0; i < nscan; i++) { |
---|
| 1715 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
| 1716 | if (subt.nrow()==0) { |
---|
[1819] | 1717 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
| 1718 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1719 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1720 | ret = 1; |
---|
| 1721 | break; |
---|
| 1722 | } |
---|
| 1723 | ROTableRow row(subt); |
---|
| 1724 | const TableRecord& rec = row.get(0); |
---|
| 1725 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
| 1726 | int laston1 = rec.asuInt("LASTON"); |
---|
| 1727 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
| 1728 | if ( i < nscan-1 ) { |
---|
| 1729 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
| 1730 | if ( subt2.nrow() == 0) { |
---|
[1819] | 1731 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1732 | |
---|
| 1733 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
| 1734 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1735 | ret = 1; |
---|
| 1736 | break; |
---|
| 1737 | } |
---|
| 1738 | ROTableRow row2(subt2); |
---|
| 1739 | const TableRecord& rec2 = row2.get(0); |
---|
| 1740 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
| 1741 | int laston2 = rec2.asuInt("LASTON"); |
---|
| 1742 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
| 1743 | if (laston1 == laston2) { |
---|
[1819] | 1744 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1745 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1746 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1747 | i +=1; |
---|
| 1748 | } |
---|
| 1749 | else { |
---|
[1819] | 1750 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1751 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1752 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1753 | } |
---|
| 1754 | } |
---|
| 1755 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
| 1756 | if (laston1 == laston2) { |
---|
[1819] | 1757 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1758 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
| 1759 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
[1391] | 1760 | ret = 1; |
---|
| 1761 | break; |
---|
| 1762 | } |
---|
| 1763 | } |
---|
| 1764 | else { |
---|
[1819] | 1765 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1766 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
| 1767 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
[1391] | 1768 | ret = 1; |
---|
| 1769 | break; |
---|
| 1770 | } |
---|
| 1771 | } |
---|
| 1772 | } |
---|
| 1773 | else { |
---|
[1819] | 1774 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1775 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
| 1776 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
[1391] | 1777 | } |
---|
| 1778 | //if ( i >= nscan ) break; |
---|
| 1779 | } |
---|
| 1780 | } |
---|
| 1781 | else { |
---|
[1819] | 1782 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1783 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
| 1784 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
[1391] | 1785 | ret = 1; |
---|
| 1786 | } |
---|
| 1787 | return ret; |
---|
| 1788 | } |
---|
| 1789 | |
---|
[1730] | 1790 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
[1391] | 1791 | { |
---|
| 1792 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
| 1793 | std::vector<double> dir; |
---|
| 1794 | Dir.tovector(dir); |
---|
| 1795 | return dir; |
---|
| 1796 | } |
---|
| 1797 | |
---|
[1819] | 1798 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
| 1799 | throw( casa::AipsError ) |
---|
| 1800 | { |
---|
| 1801 | // assumed that all rows have same nChan |
---|
| 1802 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1803 | int nChan = arr.nelements() ; |
---|
| 1804 | |
---|
| 1805 | // if nmin < 0 or nmax < 0, nothing to do |
---|
| 1806 | if ( nmin < 0 ) { |
---|
| 1807 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1808 | } |
---|
| 1809 | if ( nmax < 0 ) { |
---|
| 1810 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1811 | } |
---|
| 1812 | |
---|
| 1813 | // if nmin > nmax, exchange values |
---|
| 1814 | if ( nmin > nmax ) { |
---|
| 1815 | int tmp = nmax ; |
---|
| 1816 | nmax = nmin ; |
---|
| 1817 | nmin = tmp ; |
---|
| 1818 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1819 | os << "Swap values. Applied range is [" |
---|
| 1820 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
| 1821 | } |
---|
| 1822 | |
---|
| 1823 | // if nmin exceeds nChan, nothing to do |
---|
| 1824 | if ( nmin >= nChan ) { |
---|
| 1825 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
| 1826 | } |
---|
| 1827 | |
---|
| 1828 | // if nmax exceeds nChan, reset nmax to nChan |
---|
| 1829 | if ( nmax >= nChan ) { |
---|
| 1830 | if ( nmin == 0 ) { |
---|
| 1831 | // nothing to do |
---|
| 1832 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1833 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
| 1834 | return ; |
---|
| 1835 | } |
---|
| 1836 | else { |
---|
| 1837 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1838 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
| 1839 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
| 1840 | nmax = nChan - 1 ; |
---|
| 1841 | } |
---|
| 1842 | } |
---|
| 1843 | |
---|
| 1844 | // reshape specCol_ and flagCol_ |
---|
| 1845 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1846 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
| 1847 | } |
---|
| 1848 | |
---|
| 1849 | // update FREQUENCIES subtable |
---|
| 1850 | Double refpix ; |
---|
| 1851 | Double refval ; |
---|
| 1852 | Double increment ; |
---|
[2346] | 1853 | int freqnrow = freqTable_.table().nrow() ; |
---|
[1819] | 1854 | Vector<uInt> oldId( freqnrow ) ; |
---|
| 1855 | Vector<uInt> newId( freqnrow ) ; |
---|
| 1856 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
[2346] | 1857 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
[1819] | 1858 | /*** |
---|
| 1859 | * need to shift refpix to nmin |
---|
| 1860 | * note that channel nmin in old index will be channel 0 in new one |
---|
| 1861 | ***/ |
---|
| 1862 | refval = refval - ( refpix - nmin ) * increment ; |
---|
| 1863 | refpix = 0 ; |
---|
[2346] | 1864 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
[1819] | 1865 | } |
---|
| 1866 | |
---|
| 1867 | // update nchan |
---|
| 1868 | int newsize = nmax - nmin + 1 ; |
---|
| 1869 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
| 1870 | |
---|
| 1871 | // update bandwidth |
---|
| 1872 | // assumed all spectra in the scantable have same bandwidth |
---|
| 1873 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
| 1874 | |
---|
| 1875 | return ; |
---|
| 1876 | } |
---|
| 1877 | |
---|
| 1878 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
| 1879 | { |
---|
| 1880 | // reshape specCol_ and flagCol_ |
---|
| 1881 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1882 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
[2475] | 1883 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
[1819] | 1884 | uInt newsize = nmax - nmin + 1 ; |
---|
[2475] | 1885 | Slice slice( nmin, newsize, 1 ) ; |
---|
| 1886 | specCol_.put( irow, oldspec( slice ) ) ; |
---|
| 1887 | flagsCol_.put( irow, oldflag( slice ) ) ; |
---|
| 1888 | if ( oldspec.size() == oldtsys.size() ) |
---|
| 1889 | tsysCol_.put( irow, oldtsys( slice ) ) ; |
---|
[1819] | 1890 | |
---|
| 1891 | return ; |
---|
| 1892 | } |
---|
| 1893 | |
---|
[2435] | 1894 | void asap::Scantable::regridSpecChannel( double dnu, int nChan ) |
---|
| 1895 | { |
---|
| 1896 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1897 | os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ; |
---|
| 1898 | int freqnrow = freqTable_.table().nrow() ; |
---|
| 1899 | Vector<bool> firstTime( freqnrow, true ) ; |
---|
| 1900 | double oldincr, factor; |
---|
| 1901 | uInt currId; |
---|
| 1902 | Double refpix ; |
---|
| 1903 | Double refval ; |
---|
| 1904 | Double increment ; |
---|
| 1905 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1906 | currId = mfreqidCol_(irow); |
---|
| 1907 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1908 | if (nChan < 0) { |
---|
| 1909 | int oldsize = abcissa.size() ; |
---|
| 1910 | double bw = (abcissa[oldsize-1]-abcissa[0]) + \ |
---|
| 1911 | 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ; |
---|
| 1912 | nChan = int( ceil( abs(bw/dnu) ) ) ; |
---|
| 1913 | } |
---|
| 1914 | // actual regridding |
---|
| 1915 | regridChannel( nChan, dnu, irow ) ; |
---|
[2433] | 1916 | |
---|
[2435] | 1917 | // update FREQUENCIES subtable |
---|
| 1918 | if (firstTime[currId]) { |
---|
| 1919 | oldincr = abcissa[1]-abcissa[0] ; |
---|
| 1920 | factor = dnu/oldincr ; |
---|
| 1921 | firstTime[currId] = false ; |
---|
| 1922 | freqTable_.getEntry( refpix, refval, increment, currId ) ; |
---|
[2463] | 1923 | |
---|
[2437] | 1924 | //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ; |
---|
[2463] | 1925 | if (factor > 0 ) { |
---|
[2462] | 1926 | refpix = (refpix + 0.5)/factor - 0.5; |
---|
| 1927 | } else { |
---|
[2463] | 1928 | refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5; |
---|
[2462] | 1929 | } |
---|
[2435] | 1930 | freqTable_.setEntry( refpix, refval, increment*factor, currId ) ; |
---|
[2463] | 1931 | //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ; |
---|
| 1932 | //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ; |
---|
[2435] | 1933 | } |
---|
| 1934 | } |
---|
| 1935 | } |
---|
| 1936 | |
---|
[1819] | 1937 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
| 1938 | { |
---|
| 1939 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1940 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
| 1941 | // assumed that all rows have same nChan |
---|
| 1942 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1943 | int oldsize = arr.nelements() ; |
---|
| 1944 | |
---|
| 1945 | // if oldsize == nChan, nothing to do |
---|
| 1946 | if ( oldsize == nChan ) { |
---|
| 1947 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
| 1948 | return ; |
---|
| 1949 | } |
---|
| 1950 | |
---|
| 1951 | // if oldChan < nChan, unphysical operation |
---|
| 1952 | if ( oldsize < nChan ) { |
---|
| 1953 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
| 1954 | return ; |
---|
| 1955 | } |
---|
| 1956 | |
---|
[2433] | 1957 | // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary) |
---|
[1819] | 1958 | vector<string> coordinfo = getCoordInfo() ; |
---|
| 1959 | string oldinfo = coordinfo[0] ; |
---|
| 1960 | coordinfo[0] = "Hz" ; |
---|
| 1961 | setCoordInfo( coordinfo ) ; |
---|
| 1962 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1963 | regridChannel( nChan, dnu, irow ) ; |
---|
| 1964 | } |
---|
| 1965 | coordinfo[0] = oldinfo ; |
---|
| 1966 | setCoordInfo( coordinfo ) ; |
---|
| 1967 | |
---|
| 1968 | |
---|
| 1969 | // NOTE: this method does not update metadata such as |
---|
| 1970 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
| 1971 | |
---|
| 1972 | return ; |
---|
| 1973 | } |
---|
| 1974 | |
---|
| 1975 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
| 1976 | { |
---|
| 1977 | // logging |
---|
| 1978 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
| 1979 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
| 1980 | |
---|
| 1981 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1982 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
[2431] | 1983 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
[1819] | 1984 | Vector<Float> newspec( nChan, 0 ) ; |
---|
[2431] | 1985 | Vector<uChar> newflag( nChan, true ) ; |
---|
| 1986 | Vector<Float> newtsys ; |
---|
| 1987 | bool regridTsys = false ; |
---|
| 1988 | if (oldtsys.size() == oldspec.size()) { |
---|
| 1989 | regridTsys = true ; |
---|
| 1990 | newtsys.resize(nChan,false) ; |
---|
| 1991 | newtsys = 0 ; |
---|
| 1992 | } |
---|
[1819] | 1993 | |
---|
| 1994 | // regrid |
---|
| 1995 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1996 | int oldsize = abcissa.size() ; |
---|
| 1997 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
[2462] | 1998 | //int ichan = 0 ; |
---|
[1819] | 1999 | double wsum = 0.0 ; |
---|
[2433] | 2000 | Vector<double> zi( nChan+1 ) ; |
---|
| 2001 | Vector<double> yi( oldsize + 1 ) ; |
---|
[1819] | 2002 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
[2431] | 2003 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
[2433] | 2004 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
| 2005 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
| 2006 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
[2462] | 2007 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 2008 | zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
| 2009 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
| 2010 | zi[ii] = zi[0] + dnu * ii ; |
---|
| 2011 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
| 2012 | // Access zi and yi in ascending order |
---|
| 2013 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
| 2014 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
| 2015 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
| 2016 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
| 2017 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
| 2018 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
| 2019 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
| 2020 | int ii = izs ; |
---|
| 2021 | while (ii != ize) { |
---|
| 2022 | // always zl < zr |
---|
| 2023 | double zl = zi[ii] ; |
---|
| 2024 | double zr = zi[ii+izincr] ; |
---|
| 2025 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
| 2026 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
| 2027 | int i = min(ii, ii+izincr) ; |
---|
| 2028 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
| 2029 | int jj = ichan ; |
---|
| 2030 | while (jj != iye) { |
---|
| 2031 | // always yl < yr |
---|
| 2032 | double yl = yi[jj] ; |
---|
| 2033 | double yr = yi[jj+iyincr] ; |
---|
| 2034 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
| 2035 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
| 2036 | int j = min(jj, jj+iyincr) ; |
---|
| 2037 | if ( yr <= zl ) { |
---|
| 2038 | jj += iyincr ; |
---|
| 2039 | continue ; |
---|
[1819] | 2040 | } |
---|
[2462] | 2041 | else if ( yl <= zl ) { |
---|
| 2042 | if ( yr < zr ) { |
---|
| 2043 | if (!oldflag[j]) { |
---|
| 2044 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
| 2045 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
| 2046 | wsum += ( yr - zl ) ; |
---|
| 2047 | } |
---|
| 2048 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2049 | } |
---|
| 2050 | else { |
---|
| 2051 | if (!oldflag[j]) { |
---|
| 2052 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
| 2053 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
| 2054 | wsum += abs(dnu) ; |
---|
| 2055 | } |
---|
| 2056 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2057 | ichan = jj ; |
---|
| 2058 | break ; |
---|
| 2059 | } |
---|
[2431] | 2060 | } |
---|
[2462] | 2061 | else if ( yl < zr ) { |
---|
| 2062 | if ( yr <= zr ) { |
---|
| 2063 | if (!oldflag[j]) { |
---|
| 2064 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
| 2065 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
| 2066 | wsum += ( yr - yl ) ; |
---|
| 2067 | } |
---|
| 2068 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2069 | } |
---|
| 2070 | else { |
---|
| 2071 | if (!oldflag[j]) { |
---|
| 2072 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
| 2073 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
| 2074 | wsum += ( zr - yl ) ; |
---|
| 2075 | } |
---|
| 2076 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2077 | ichan = jj ; |
---|
| 2078 | break ; |
---|
| 2079 | } |
---|
[1819] | 2080 | } |
---|
[2462] | 2081 | else { |
---|
| 2082 | ichan = jj - iyincr ; |
---|
| 2083 | break ; |
---|
[2431] | 2084 | } |
---|
[2462] | 2085 | jj += iyincr ; |
---|
[1819] | 2086 | } |
---|
[2462] | 2087 | if ( wsum != 0.0 ) { |
---|
| 2088 | newspec[i] /= wsum ; |
---|
| 2089 | if (regridTsys) newtsys[i] /= wsum ; |
---|
| 2090 | } |
---|
| 2091 | wsum = 0.0 ; |
---|
| 2092 | ii += izincr ; |
---|
[1819] | 2093 | } |
---|
[2462] | 2094 | // if ( dnu > 0.0 ) { |
---|
| 2095 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 2096 | // double zl = zi[ii] ; |
---|
| 2097 | // double zr = zi[ii+1] ; |
---|
| 2098 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 2099 | // double yl = yi[j] ; |
---|
| 2100 | // double yr = yi[j+1] ; |
---|
| 2101 | // if ( yl <= zl ) { |
---|
| 2102 | // if ( yr <= zl ) { |
---|
| 2103 | // continue ; |
---|
| 2104 | // } |
---|
| 2105 | // else if ( yr <= zr ) { |
---|
| 2106 | // if (!oldflag[j]) { |
---|
| 2107 | // newspec[ii] += oldspec[j] * ( yr - zl ) ; |
---|
| 2108 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ; |
---|
| 2109 | // wsum += ( yr - zl ) ; |
---|
| 2110 | // } |
---|
| 2111 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2112 | // } |
---|
| 2113 | // else { |
---|
| 2114 | // if (!oldflag[j]) { |
---|
| 2115 | // newspec[ii] += oldspec[j] * dnu ; |
---|
| 2116 | // if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ; |
---|
| 2117 | // wsum += dnu ; |
---|
| 2118 | // } |
---|
| 2119 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2120 | // ichan = j ; |
---|
| 2121 | // break ; |
---|
| 2122 | // } |
---|
| 2123 | // } |
---|
| 2124 | // else if ( yl < zr ) { |
---|
| 2125 | // if ( yr <= zr ) { |
---|
| 2126 | // if (!oldflag[j]) { |
---|
| 2127 | // newspec[ii] += oldspec[j] * ( yr - yl ) ; |
---|
| 2128 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ; |
---|
| 2129 | // wsum += ( yr - yl ) ; |
---|
| 2130 | // } |
---|
| 2131 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2132 | // } |
---|
| 2133 | // else { |
---|
| 2134 | // if (!oldflag[j]) { |
---|
| 2135 | // newspec[ii] += oldspec[j] * ( zr - yl ) ; |
---|
| 2136 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ; |
---|
| 2137 | // wsum += ( zr - yl ) ; |
---|
| 2138 | // } |
---|
| 2139 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2140 | // ichan = j ; |
---|
| 2141 | // break ; |
---|
| 2142 | // } |
---|
| 2143 | // } |
---|
| 2144 | // else { |
---|
| 2145 | // ichan = j - 1 ; |
---|
| 2146 | // break ; |
---|
| 2147 | // } |
---|
| 2148 | // } |
---|
| 2149 | // if ( wsum != 0.0 ) { |
---|
| 2150 | // newspec[ii] /= wsum ; |
---|
| 2151 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
| 2152 | // } |
---|
| 2153 | // wsum = 0.0 ; |
---|
| 2154 | // } |
---|
[1819] | 2155 | // } |
---|
[2462] | 2156 | // else if ( dnu < 0.0 ) { |
---|
| 2157 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
---|
| 2158 | // double zl = zi[ii] ; |
---|
| 2159 | // double zr = zi[ii+1] ; |
---|
| 2160 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
---|
| 2161 | // double yl = yi[j] ; |
---|
| 2162 | // double yr = yi[j+1] ; |
---|
| 2163 | // if ( yl >= zl ) { |
---|
| 2164 | // if ( yr >= zl ) { |
---|
| 2165 | // continue ; |
---|
| 2166 | // } |
---|
| 2167 | // else if ( yr >= zr ) { |
---|
| 2168 | // if (!oldflag[j]) { |
---|
| 2169 | // newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
---|
| 2170 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ; |
---|
| 2171 | // wsum += abs( yr - zl ) ; |
---|
| 2172 | // } |
---|
| 2173 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2174 | // } |
---|
| 2175 | // else { |
---|
| 2176 | // if (!oldflag[j]) { |
---|
| 2177 | // newspec[ii] += oldspec[j] * abs( dnu ) ; |
---|
| 2178 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ; |
---|
| 2179 | // wsum += abs( dnu ) ; |
---|
| 2180 | // } |
---|
| 2181 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2182 | // ichan = j ; |
---|
| 2183 | // break ; |
---|
| 2184 | // } |
---|
| 2185 | // } |
---|
| 2186 | // else if ( yl > zr ) { |
---|
| 2187 | // if ( yr >= zr ) { |
---|
| 2188 | // if (!oldflag[j]) { |
---|
| 2189 | // newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
---|
| 2190 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ; |
---|
| 2191 | // wsum += abs( yr - yl ) ; |
---|
| 2192 | // } |
---|
| 2193 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2194 | // } |
---|
| 2195 | // else { |
---|
| 2196 | // if (!oldflag[j]) { |
---|
| 2197 | // newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
---|
| 2198 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ; |
---|
| 2199 | // wsum += abs( zr - yl ) ; |
---|
| 2200 | // } |
---|
| 2201 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
---|
| 2202 | // ichan = j ; |
---|
| 2203 | // break ; |
---|
| 2204 | // } |
---|
| 2205 | // } |
---|
| 2206 | // else { |
---|
| 2207 | // ichan = j - 1 ; |
---|
| 2208 | // break ; |
---|
| 2209 | // } |
---|
| 2210 | // } |
---|
| 2211 | // if ( wsum != 0.0 ) { |
---|
| 2212 | // newspec[ii] /= wsum ; |
---|
| 2213 | // if (regridTsys) newtsys[ii] /= wsum ; |
---|
| 2214 | // } |
---|
| 2215 | // wsum = 0.0 ; |
---|
[1819] | 2216 | // } |
---|
| 2217 | // } |
---|
[2462] | 2218 | // // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
---|
| 2219 | // // pile += dnu ; |
---|
| 2220 | // // wedge = olddnu * ( refChan + 1 ) ; |
---|
| 2221 | // // while ( wedge < pile ) { |
---|
| 2222 | // // newspec[0] += olddnu * oldspec[refChan] ; |
---|
| 2223 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2224 | // // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
---|
| 2225 | // // refChan++ ; |
---|
| 2226 | // // wedge += olddnu ; |
---|
| 2227 | // // wsum += olddnu ; |
---|
| 2228 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2229 | // // } |
---|
| 2230 | // // frac = ( wedge - pile ) / olddnu ; |
---|
| 2231 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2232 | // // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2233 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
---|
| 2234 | // // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2235 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
---|
| 2236 | // // newspec[0] /= wsum ; |
---|
| 2237 | // // //ofs << "newspec[0] = " << newspec[0] << endl ; |
---|
| 2238 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
[1819] | 2239 | |
---|
[2462] | 2240 | // // /*** |
---|
| 2241 | // // * ichan = 1 - nChan-2 |
---|
| 2242 | // // ***/ |
---|
| 2243 | // // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
---|
| 2244 | // // pile += dnu ; |
---|
| 2245 | // // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
---|
| 2246 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2247 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
---|
| 2248 | // // refChan++ ; |
---|
| 2249 | // // wedge += olddnu ; |
---|
| 2250 | // // wsum = frac * olddnu ; |
---|
| 2251 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2252 | // // while ( wedge < pile ) { |
---|
| 2253 | // // newspec[ichan] += olddnu * oldspec[refChan] ; |
---|
| 2254 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2255 | // // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
---|
| 2256 | // // refChan++ ; |
---|
| 2257 | // // wedge += olddnu ; |
---|
| 2258 | // // wsum += olddnu ; |
---|
| 2259 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2260 | // // } |
---|
| 2261 | // // frac = ( wedge - pile ) / olddnu ; |
---|
| 2262 | // // wsum += ( 1.0 - frac ) * olddnu ; |
---|
| 2263 | // // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
---|
| 2264 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
---|
| 2265 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2266 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2267 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2268 | // // newspec[ichan] /= wsum ; |
---|
| 2269 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
---|
| 2270 | // // } |
---|
[1819] | 2271 | |
---|
[2462] | 2272 | // // /*** |
---|
| 2273 | // // * ichan = nChan-1 |
---|
| 2274 | // // ***/ |
---|
| 2275 | // // // NOTE: Assumed that all spectra have the same bandwidth |
---|
| 2276 | // // pile += dnu ; |
---|
| 2277 | // // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
| 2278 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
| 2279 | // // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2280 | // // refChan++ ; |
---|
| 2281 | // // wedge += olddnu ; |
---|
| 2282 | // // wsum = frac * olddnu ; |
---|
| 2283 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2284 | // // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
| 2285 | // // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
| 2286 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
| 2287 | // // wsum += olddnu ; |
---|
| 2288 | // // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2289 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2290 | // // } |
---|
| 2291 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2292 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2293 | // // newspec[nChan-1] /= wsum ; |
---|
| 2294 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
[1819] | 2295 | |
---|
[2462] | 2296 | // // // ofs.close() ; |
---|
| 2297 | |
---|
[2032] | 2298 | specCol_.put( irow, newspec ) ; |
---|
| 2299 | flagsCol_.put( irow, newflag ) ; |
---|
[2431] | 2300 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
[1819] | 2301 | |
---|
| 2302 | return ; |
---|
| 2303 | } |
---|
| 2304 | |
---|
[1730] | 2305 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
| 2306 | { |
---|
| 2307 | std::vector<float> out(5); |
---|
| 2308 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
| 2309 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
| 2310 | mweatheridCol_(uInt(whichrow))); |
---|
| 2311 | |
---|
| 2312 | |
---|
| 2313 | return out; |
---|
[1391] | 2314 | } |
---|
[1730] | 2315 | |
---|
[2047] | 2316 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
[1907] | 2317 | { |
---|
| 2318 | uChar flag; |
---|
| 2319 | Vector<uChar> flags; |
---|
[2047] | 2320 | flagsCol_.get(whichrow, flags); |
---|
[2012] | 2321 | flag = flags[0]; |
---|
[2047] | 2322 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
[2012] | 2323 | flag &= flags[i]; |
---|
| 2324 | } |
---|
| 2325 | return ((flag >> 7) == 1); |
---|
| 2326 | } |
---|
| 2327 | |
---|
[2277] | 2328 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2329 | { |
---|
[2193] | 2330 | try { |
---|
| 2331 | ofstream ofs; |
---|
| 2332 | String coordInfo = ""; |
---|
| 2333 | bool hasSameNchan = true; |
---|
| 2334 | bool outTextFile = false; |
---|
[2640] | 2335 | bool csvFormat = false; |
---|
[2047] | 2336 | |
---|
[2193] | 2337 | if (blfile != "") { |
---|
[2640] | 2338 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2339 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 2340 | if (ofs) outTextFile = true; |
---|
| 2341 | } |
---|
[2047] | 2342 | |
---|
[2193] | 2343 | if (outLogger || outTextFile) { |
---|
| 2344 | coordInfo = getCoordInfo()[0]; |
---|
| 2345 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2346 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2347 | } |
---|
[2047] | 2348 | |
---|
[2193] | 2349 | Fitter fitter = Fitter(); |
---|
| 2350 | fitter.setExpression("poly", order); |
---|
| 2351 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2352 | |
---|
[2193] | 2353 | int nRow = nrow(); |
---|
| 2354 | std::vector<bool> chanMask; |
---|
| 2355 | bool showProgress; |
---|
| 2356 | int minNRow; |
---|
| 2357 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2047] | 2358 | |
---|
[2193] | 2359 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2360 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2361 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2362 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2640] | 2363 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
[2193] | 2364 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2365 | } |
---|
| 2366 | |
---|
| 2367 | if (outTextFile) ofs.close(); |
---|
| 2368 | |
---|
| 2369 | } catch (...) { |
---|
| 2370 | throw; |
---|
[2047] | 2371 | } |
---|
| 2372 | } |
---|
| 2373 | |
---|
[2189] | 2374 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2375 | { |
---|
[2193] | 2376 | try { |
---|
| 2377 | ofstream ofs; |
---|
| 2378 | String coordInfo = ""; |
---|
| 2379 | bool hasSameNchan = true; |
---|
| 2380 | bool outTextFile = false; |
---|
[2640] | 2381 | bool csvFormat = false; |
---|
[2047] | 2382 | |
---|
[2193] | 2383 | if (blfile != "") { |
---|
[2640] | 2384 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2385 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 2386 | if (ofs) outTextFile = true; |
---|
| 2387 | } |
---|
[2047] | 2388 | |
---|
[2193] | 2389 | if (outLogger || outTextFile) { |
---|
| 2390 | coordInfo = getCoordInfo()[0]; |
---|
| 2391 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2392 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2393 | } |
---|
[2047] | 2394 | |
---|
[2193] | 2395 | Fitter fitter = Fitter(); |
---|
| 2396 | fitter.setExpression("poly", order); |
---|
| 2397 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2398 | |
---|
[2193] | 2399 | int nRow = nrow(); |
---|
| 2400 | std::vector<bool> chanMask; |
---|
| 2401 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2402 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2403 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2047] | 2404 | |
---|
[2193] | 2405 | bool showProgress; |
---|
| 2406 | int minNRow; |
---|
| 2407 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2408 | |
---|
[2193] | 2409 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2047] | 2410 | |
---|
[2193] | 2411 | //------------------------------------------------------- |
---|
| 2412 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2413 | //------------------------------------------------------- |
---|
| 2414 | int edgeSize = edge.size(); |
---|
| 2415 | std::vector<int> currentEdge; |
---|
| 2416 | if (edgeSize >= 2) { |
---|
| 2417 | int idx = 0; |
---|
| 2418 | if (edgeSize > 2) { |
---|
| 2419 | if (edgeSize < minEdgeSize) { |
---|
| 2420 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2421 | } |
---|
| 2422 | idx = 2 * getIF(whichrow); |
---|
[2047] | 2423 | } |
---|
[2193] | 2424 | currentEdge.push_back(edge[idx]); |
---|
| 2425 | currentEdge.push_back(edge[idx+1]); |
---|
| 2426 | } else { |
---|
| 2427 | throw(AipsError("Wrong length of edge element")); |
---|
[2047] | 2428 | } |
---|
[2193] | 2429 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2430 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2431 | chanMask = lineFinder.getMask(); |
---|
| 2432 | //------------------------------------------------------- |
---|
| 2433 | |
---|
| 2434 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2435 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2436 | |
---|
[2640] | 2437 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
[2193] | 2438 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2047] | 2439 | } |
---|
| 2440 | |
---|
[2193] | 2441 | if (outTextFile) ofs.close(); |
---|
[2047] | 2442 | |
---|
[2193] | 2443 | } catch (...) { |
---|
| 2444 | throw; |
---|
[2047] | 2445 | } |
---|
| 2446 | } |
---|
| 2447 | |
---|
[2189] | 2448 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2081] | 2449 | { |
---|
[2193] | 2450 | try { |
---|
| 2451 | ofstream ofs; |
---|
| 2452 | String coordInfo = ""; |
---|
| 2453 | bool hasSameNchan = true; |
---|
| 2454 | bool outTextFile = false; |
---|
[2640] | 2455 | bool csvFormat = false; |
---|
[2012] | 2456 | |
---|
[2193] | 2457 | if (blfile != "") { |
---|
[2640] | 2458 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2459 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 2460 | if (ofs) outTextFile = true; |
---|
| 2461 | } |
---|
[2012] | 2462 | |
---|
[2193] | 2463 | if (outLogger || outTextFile) { |
---|
| 2464 | coordInfo = getCoordInfo()[0]; |
---|
| 2465 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2466 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2467 | } |
---|
[2012] | 2468 | |
---|
[2193] | 2469 | //Fitter fitter = Fitter(); |
---|
| 2470 | //fitter.setExpression("cspline", nPiece); |
---|
| 2471 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2472 | |
---|
[2193] | 2473 | bool showProgress; |
---|
| 2474 | int minNRow; |
---|
| 2475 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2012] | 2476 | |
---|
[2344] | 2477 | int nRow = nrow(); |
---|
| 2478 | std::vector<bool> chanMask; |
---|
| 2479 | |
---|
| 2480 | //-------------------------------- |
---|
[2193] | 2481 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2482 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2483 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2484 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2344] | 2485 | std::vector<int> pieceEdges(nPiece+1); |
---|
| 2486 | std::vector<float> params(nPiece*4); |
---|
[2193] | 2487 | int nClipped = 0; |
---|
| 2488 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2489 | setSpectrum(res, whichrow); |
---|
| 2490 | // |
---|
[2012] | 2491 | |
---|
[2640] | 2492 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
[2193] | 2493 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2494 | } |
---|
[2344] | 2495 | //-------------------------------- |
---|
| 2496 | |
---|
[2193] | 2497 | if (outTextFile) ofs.close(); |
---|
| 2498 | |
---|
| 2499 | } catch (...) { |
---|
| 2500 | throw; |
---|
[2012] | 2501 | } |
---|
| 2502 | } |
---|
| 2503 | |
---|
[2189] | 2504 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 2505 | { |
---|
[2193] | 2506 | try { |
---|
| 2507 | ofstream ofs; |
---|
| 2508 | String coordInfo = ""; |
---|
| 2509 | bool hasSameNchan = true; |
---|
| 2510 | bool outTextFile = false; |
---|
[2640] | 2511 | bool csvFormat = false; |
---|
[2012] | 2512 | |
---|
[2193] | 2513 | if (blfile != "") { |
---|
[2640] | 2514 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2515 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 2516 | if (ofs) outTextFile = true; |
---|
| 2517 | } |
---|
[2012] | 2518 | |
---|
[2193] | 2519 | if (outLogger || outTextFile) { |
---|
| 2520 | coordInfo = getCoordInfo()[0]; |
---|
| 2521 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2522 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2523 | } |
---|
[2012] | 2524 | |
---|
[2193] | 2525 | //Fitter fitter = Fitter(); |
---|
| 2526 | //fitter.setExpression("cspline", nPiece); |
---|
| 2527 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 2528 | |
---|
[2193] | 2529 | int nRow = nrow(); |
---|
| 2530 | std::vector<bool> chanMask; |
---|
| 2531 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2532 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2533 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 2534 | |
---|
[2193] | 2535 | bool showProgress; |
---|
| 2536 | int minNRow; |
---|
| 2537 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2538 | |
---|
[2193] | 2539 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 2540 | |
---|
[2193] | 2541 | //------------------------------------------------------- |
---|
| 2542 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2543 | //------------------------------------------------------- |
---|
| 2544 | int edgeSize = edge.size(); |
---|
| 2545 | std::vector<int> currentEdge; |
---|
| 2546 | if (edgeSize >= 2) { |
---|
| 2547 | int idx = 0; |
---|
| 2548 | if (edgeSize > 2) { |
---|
| 2549 | if (edgeSize < minEdgeSize) { |
---|
| 2550 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2551 | } |
---|
| 2552 | idx = 2 * getIF(whichrow); |
---|
[2012] | 2553 | } |
---|
[2193] | 2554 | currentEdge.push_back(edge[idx]); |
---|
| 2555 | currentEdge.push_back(edge[idx+1]); |
---|
| 2556 | } else { |
---|
| 2557 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 2558 | } |
---|
[2193] | 2559 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2560 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2561 | chanMask = lineFinder.getMask(); |
---|
| 2562 | //------------------------------------------------------- |
---|
| 2563 | |
---|
| 2564 | |
---|
| 2565 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2566 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2344] | 2567 | std::vector<int> pieceEdges(nPiece+1); |
---|
| 2568 | std::vector<float> params(nPiece*4); |
---|
[2193] | 2569 | int nClipped = 0; |
---|
| 2570 | std::vector<float> res = doCubicSplineFitting(getSpectrum(whichrow), chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 2571 | setSpectrum(res, whichrow); |
---|
| 2572 | // |
---|
| 2573 | |
---|
[2640] | 2574 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
[2193] | 2575 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[1907] | 2576 | } |
---|
[2012] | 2577 | |
---|
[2193] | 2578 | if (outTextFile) ofs.close(); |
---|
[2012] | 2579 | |
---|
[2193] | 2580 | } catch (...) { |
---|
| 2581 | throw; |
---|
[2012] | 2582 | } |
---|
[1730] | 2583 | } |
---|
[1907] | 2584 | |
---|
[2193] | 2585 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 2586 | { |
---|
| 2587 | if (data.size() != mask.size()) { |
---|
| 2588 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 2589 | } |
---|
[2012] | 2590 | if (nPiece < 1) { |
---|
[2094] | 2591 | throw(AipsError("number of the sections must be one or more")); |
---|
[2012] | 2592 | } |
---|
| 2593 | |
---|
| 2594 | int nChan = data.size(); |
---|
[2344] | 2595 | std::vector<int> maskArray(nChan); |
---|
| 2596 | std::vector<int> x(nChan); |
---|
| 2597 | int j = 0; |
---|
[2012] | 2598 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 2599 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2012] | 2600 | if (mask[i]) { |
---|
[2344] | 2601 | x[j] = i; |
---|
| 2602 | j++; |
---|
[2012] | 2603 | } |
---|
| 2604 | } |
---|
[2344] | 2605 | int initNData = j; |
---|
[2012] | 2606 | |
---|
[2193] | 2607 | if (initNData < nPiece) { |
---|
| 2608 | throw(AipsError("too few non-flagged channels")); |
---|
| 2609 | } |
---|
[2081] | 2610 | |
---|
| 2611 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
[2344] | 2612 | std::vector<double> invEdge(nPiece-1); |
---|
| 2613 | idxEdge[0] = x[0]; |
---|
[2012] | 2614 | for (int i = 1; i < nPiece; ++i) { |
---|
[2047] | 2615 | int valX = x[nElement*i]; |
---|
[2344] | 2616 | idxEdge[i] = valX; |
---|
| 2617 | invEdge[i-1] = 1.0/(double)valX; |
---|
[2012] | 2618 | } |
---|
[2344] | 2619 | idxEdge[nPiece] = x[initNData-1]+1; |
---|
[2064] | 2620 | |
---|
[2081] | 2621 | int nData = initNData; |
---|
| 2622 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
| 2623 | |
---|
[2344] | 2624 | std::vector<double> x1(nChan), x2(nChan), x3(nChan); |
---|
| 2625 | std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan); |
---|
| 2626 | std::vector<double> r1(nChan), residual(nChan); |
---|
[2012] | 2627 | for (int i = 0; i < nChan; ++i) { |
---|
[2064] | 2628 | double di = (double)i; |
---|
| 2629 | double dD = (double)data[i]; |
---|
[2344] | 2630 | x1[i] = di; |
---|
| 2631 | x2[i] = di*di; |
---|
| 2632 | x3[i] = di*di*di; |
---|
| 2633 | z1[i] = dD; |
---|
| 2634 | x1z1[i] = dD*di; |
---|
| 2635 | x2z1[i] = dD*di*di; |
---|
| 2636 | x3z1[i] = dD*di*di*di; |
---|
| 2637 | r1[i] = 0.0; |
---|
| 2638 | residual[i] = 0.0; |
---|
[2012] | 2639 | } |
---|
| 2640 | |
---|
| 2641 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2064] | 2642 | // xMatrix : horizontal concatenation of |
---|
| 2643 | // the least-sq. matrix (left) and an |
---|
| 2644 | // identity matrix (right). |
---|
| 2645 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2012] | 2646 | double xMatrix[nDOF][2*nDOF]; |
---|
| 2647 | double zMatrix[nDOF]; |
---|
| 2648 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2649 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 2650 | xMatrix[i][j] = 0.0; |
---|
| 2651 | } |
---|
| 2652 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 2653 | zMatrix[i] = 0.0; |
---|
| 2654 | } |
---|
| 2655 | |
---|
| 2656 | for (int n = 0; n < nPiece; ++n) { |
---|
[2193] | 2657 | int nUseDataInPiece = 0; |
---|
[2064] | 2658 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2659 | |
---|
[2012] | 2660 | if (maskArray[i] == 0) continue; |
---|
[2064] | 2661 | |
---|
[2012] | 2662 | xMatrix[0][0] += 1.0; |
---|
[2064] | 2663 | xMatrix[0][1] += x1[i]; |
---|
| 2664 | xMatrix[0][2] += x2[i]; |
---|
| 2665 | xMatrix[0][3] += x3[i]; |
---|
| 2666 | xMatrix[1][1] += x2[i]; |
---|
| 2667 | xMatrix[1][2] += x3[i]; |
---|
| 2668 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
| 2669 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
| 2670 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
| 2671 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
[2012] | 2672 | zMatrix[0] += z1[i]; |
---|
[2064] | 2673 | zMatrix[1] += x1z1[i]; |
---|
| 2674 | zMatrix[2] += x2z1[i]; |
---|
| 2675 | zMatrix[3] += x3z1[i]; |
---|
| 2676 | |
---|
[2012] | 2677 | for (int j = 0; j < n; ++j) { |
---|
[2064] | 2678 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
[2012] | 2679 | q = q*q*q; |
---|
| 2680 | xMatrix[0][j+4] += q; |
---|
[2064] | 2681 | xMatrix[1][j+4] += q*x1[i]; |
---|
| 2682 | xMatrix[2][j+4] += q*x2[i]; |
---|
| 2683 | xMatrix[3][j+4] += q*x3[i]; |
---|
[2012] | 2684 | for (int k = 0; k < j; ++k) { |
---|
[2064] | 2685 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
[2012] | 2686 | r = r*r*r; |
---|
| 2687 | xMatrix[k+4][j+4] += r*q; |
---|
| 2688 | } |
---|
| 2689 | xMatrix[j+4][j+4] += q*q; |
---|
| 2690 | zMatrix[j+4] += q*z1[i]; |
---|
| 2691 | } |
---|
[2064] | 2692 | |
---|
[2193] | 2693 | nUseDataInPiece++; |
---|
[2012] | 2694 | } |
---|
[2193] | 2695 | |
---|
| 2696 | if (nUseDataInPiece < 1) { |
---|
| 2697 | std::vector<string> suffixOfPieceNumber(4); |
---|
| 2698 | suffixOfPieceNumber[0] = "th"; |
---|
| 2699 | suffixOfPieceNumber[1] = "st"; |
---|
| 2700 | suffixOfPieceNumber[2] = "nd"; |
---|
| 2701 | suffixOfPieceNumber[3] = "rd"; |
---|
| 2702 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
| 2703 | ostringstream oss; |
---|
| 2704 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
| 2705 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
| 2706 | throw(AipsError(String(oss))); |
---|
| 2707 | } |
---|
[2012] | 2708 | } |
---|
| 2709 | |
---|
| 2710 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2711 | for (int j = 0; j < i; ++j) { |
---|
| 2712 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 2713 | } |
---|
| 2714 | } |
---|
| 2715 | |
---|
[2344] | 2716 | std::vector<double> invDiag(nDOF); |
---|
[2012] | 2717 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 2718 | invDiag[i] = 1.0/xMatrix[i][i]; |
---|
[2012] | 2719 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2720 | xMatrix[i][j] *= invDiag[i]; |
---|
| 2721 | } |
---|
| 2722 | } |
---|
| 2723 | |
---|
| 2724 | for (int k = 0; k < nDOF; ++k) { |
---|
| 2725 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2726 | if (i != k) { |
---|
| 2727 | double factor1 = xMatrix[k][k]; |
---|
| 2728 | double factor2 = xMatrix[i][k]; |
---|
| 2729 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2730 | xMatrix[i][j] *= factor1; |
---|
| 2731 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 2732 | xMatrix[i][j] /= factor1; |
---|
| 2733 | } |
---|
| 2734 | } |
---|
| 2735 | } |
---|
| 2736 | double xDiag = xMatrix[k][k]; |
---|
| 2737 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 2738 | xMatrix[k][j] /= xDiag; |
---|
| 2739 | } |
---|
| 2740 | } |
---|
| 2741 | |
---|
| 2742 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2743 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2744 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 2745 | } |
---|
| 2746 | } |
---|
| 2747 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
| 2748 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
| 2749 | //cubic terms for the other pieces (in case nPiece>1). |
---|
[2344] | 2750 | std::vector<double> y(nDOF); |
---|
[2012] | 2751 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 2752 | y[i] = 0.0; |
---|
[2012] | 2753 | for (int j = 0; j < nDOF; ++j) { |
---|
| 2754 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 2755 | } |
---|
| 2756 | } |
---|
| 2757 | |
---|
| 2758 | double a0 = y[0]; |
---|
| 2759 | double a1 = y[1]; |
---|
| 2760 | double a2 = y[2]; |
---|
| 2761 | double a3 = y[3]; |
---|
| 2762 | |
---|
[2344] | 2763 | int j = 0; |
---|
[2012] | 2764 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 2765 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 2766 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
[2012] | 2767 | } |
---|
[2344] | 2768 | params[j] = a0; |
---|
| 2769 | params[j+1] = a1; |
---|
| 2770 | params[j+2] = a2; |
---|
| 2771 | params[j+3] = a3; |
---|
| 2772 | j += 4; |
---|
[2012] | 2773 | |
---|
| 2774 | if (n == nPiece-1) break; |
---|
| 2775 | |
---|
| 2776 | double d = y[4+n]; |
---|
[2064] | 2777 | double iE = invEdge[n]; |
---|
| 2778 | a0 += d; |
---|
| 2779 | a1 -= 3.0*d*iE; |
---|
| 2780 | a2 += 3.0*d*iE*iE; |
---|
| 2781 | a3 -= d*iE*iE*iE; |
---|
[2012] | 2782 | } |
---|
| 2783 | |
---|
[2344] | 2784 | //subtract constant value for masked regions at the edge of spectrum |
---|
| 2785 | if (idxEdge[0] > 0) { |
---|
| 2786 | int n = idxEdge[0]; |
---|
| 2787 | for (int i = 0; i < idxEdge[0]; ++i) { |
---|
| 2788 | //--cubic extrapolate-- |
---|
| 2789 | //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i]; |
---|
| 2790 | //--linear extrapolate-- |
---|
| 2791 | //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 2792 | //--constant-- |
---|
| 2793 | r1[i] = r1[n]; |
---|
| 2794 | } |
---|
| 2795 | } |
---|
| 2796 | if (idxEdge[nPiece] < nChan) { |
---|
| 2797 | int n = idxEdge[nPiece]-1; |
---|
| 2798 | for (int i = idxEdge[nPiece]; i < nChan; ++i) { |
---|
| 2799 | //--cubic extrapolate-- |
---|
| 2800 | //int m = 4*(nPiece-1); |
---|
| 2801 | //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i]; |
---|
| 2802 | //--linear extrapolate-- |
---|
| 2803 | //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 2804 | //--constant-- |
---|
| 2805 | r1[i] = r1[n]; |
---|
| 2806 | } |
---|
| 2807 | } |
---|
| 2808 | |
---|
| 2809 | for (int i = 0; i < nChan; ++i) { |
---|
| 2810 | residual[i] = z1[i] - r1[i]; |
---|
| 2811 | } |
---|
| 2812 | |
---|
[2012] | 2813 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 2814 | break; |
---|
| 2815 | } else { |
---|
| 2816 | double stdDev = 0.0; |
---|
| 2817 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2818 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2012] | 2819 | } |
---|
| 2820 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 2821 | |
---|
| 2822 | double thres = stdDev * thresClip; |
---|
| 2823 | int newNData = 0; |
---|
| 2824 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 2825 | if (abs(residual[i]) >= thres) { |
---|
[2012] | 2826 | maskArray[i] = 0; |
---|
| 2827 | } |
---|
| 2828 | if (maskArray[i] > 0) { |
---|
| 2829 | newNData++; |
---|
| 2830 | } |
---|
| 2831 | } |
---|
[2081] | 2832 | if (newNData == nData) { |
---|
[2064] | 2833 | break; //no more flag to add. iteration stops. |
---|
[2012] | 2834 | } else { |
---|
[2081] | 2835 | nData = newNData; |
---|
[2012] | 2836 | } |
---|
| 2837 | } |
---|
| 2838 | } |
---|
| 2839 | |
---|
[2193] | 2840 | nClipped = initNData - nData; |
---|
| 2841 | |
---|
[2344] | 2842 | std::vector<float> result(nChan); |
---|
[2058] | 2843 | if (getResidual) { |
---|
| 2844 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 2845 | result[i] = (float)residual[i]; |
---|
[2058] | 2846 | } |
---|
| 2847 | } else { |
---|
| 2848 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 2849 | result[i] = (float)r1[i]; |
---|
[2058] | 2850 | } |
---|
[2012] | 2851 | } |
---|
| 2852 | |
---|
[2058] | 2853 | return result; |
---|
[2012] | 2854 | } |
---|
| 2855 | |
---|
[2344] | 2856 | void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2081] | 2857 | { |
---|
[2186] | 2858 | nWaves.clear(); |
---|
| 2859 | |
---|
| 2860 | if (applyFFT) { |
---|
| 2861 | string fftThAttr; |
---|
| 2862 | float fftThSigma; |
---|
| 2863 | int fftThTop; |
---|
| 2864 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
| 2865 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
| 2866 | } |
---|
| 2867 | |
---|
[2411] | 2868 | addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves); |
---|
[2186] | 2869 | } |
---|
| 2870 | |
---|
| 2871 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
| 2872 | { |
---|
| 2873 | uInt idxSigma = fftThresh.find("sigma"); |
---|
| 2874 | uInt idxTop = fftThresh.find("top"); |
---|
| 2875 | |
---|
| 2876 | if (idxSigma == fftThresh.size() - 5) { |
---|
| 2877 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
| 2878 | is >> fftThSigma; |
---|
| 2879 | fftThAttr = "sigma"; |
---|
| 2880 | } else if (idxTop == 0) { |
---|
| 2881 | std::istringstream is(fftThresh.substr(3)); |
---|
| 2882 | is >> fftThTop; |
---|
| 2883 | fftThAttr = "top"; |
---|
| 2884 | } else { |
---|
| 2885 | bool isNumber = true; |
---|
| 2886 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
| 2887 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
| 2888 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
| 2889 | isNumber = false; |
---|
| 2890 | break; |
---|
| 2891 | } |
---|
| 2892 | } |
---|
| 2893 | if (isNumber) { |
---|
| 2894 | std::istringstream is(fftThresh); |
---|
| 2895 | is >> fftThSigma; |
---|
| 2896 | fftThAttr = "sigma"; |
---|
| 2897 | } else { |
---|
| 2898 | throw(AipsError("fftthresh has a wrong value")); |
---|
| 2899 | } |
---|
| 2900 | } |
---|
| 2901 | } |
---|
| 2902 | |
---|
| 2903 | void Scantable::doSelectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftMethod, const float fftThSigma, const int fftThTop, const std::string& fftThAttr, std::vector<int>& nWaves) |
---|
| 2904 | { |
---|
| 2905 | std::vector<float> fspec; |
---|
| 2906 | if (fftMethod == "fft") { |
---|
| 2907 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
| 2908 | //} else if (fftMethod == "lsp") { |
---|
| 2909 | // fspec = lombScarglePeriodogram(whichrow); |
---|
| 2910 | } |
---|
| 2911 | |
---|
| 2912 | if (fftThAttr == "sigma") { |
---|
| 2913 | float mean = 0.0; |
---|
| 2914 | float mean2 = 0.0; |
---|
| 2915 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 2916 | mean += fspec[i]; |
---|
| 2917 | mean2 += fspec[i]*fspec[i]; |
---|
| 2918 | } |
---|
| 2919 | mean /= float(fspec.size()); |
---|
| 2920 | mean2 /= float(fspec.size()); |
---|
| 2921 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
| 2922 | |
---|
| 2923 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 2924 | if (fspec[i] >= thres) { |
---|
| 2925 | nWaves.push_back(i); |
---|
| 2926 | } |
---|
| 2927 | } |
---|
| 2928 | |
---|
| 2929 | } else if (fftThAttr == "top") { |
---|
| 2930 | for (int i = 0; i < fftThTop; ++i) { |
---|
| 2931 | float max = 0.0; |
---|
| 2932 | int maxIdx = 0; |
---|
| 2933 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
| 2934 | if (fspec[j] > max) { |
---|
| 2935 | max = fspec[j]; |
---|
| 2936 | maxIdx = j; |
---|
| 2937 | } |
---|
| 2938 | } |
---|
| 2939 | nWaves.push_back(maxIdx); |
---|
| 2940 | fspec[maxIdx] = 0.0; |
---|
| 2941 | } |
---|
| 2942 | |
---|
| 2943 | } |
---|
| 2944 | |
---|
| 2945 | if (nWaves.size() > 1) { |
---|
| 2946 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2947 | } |
---|
| 2948 | } |
---|
| 2949 | |
---|
[2411] | 2950 | void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2186] | 2951 | { |
---|
[2411] | 2952 | std::vector<int> tempAddNWaves, tempRejectNWaves; |
---|
[2186] | 2953 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
[2411] | 2954 | tempAddNWaves.push_back(addNWaves[i]); |
---|
| 2955 | } |
---|
| 2956 | if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) { |
---|
| 2957 | setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves); |
---|
| 2958 | } |
---|
| 2959 | |
---|
| 2960 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
| 2961 | tempRejectNWaves.push_back(rejectNWaves[i]); |
---|
| 2962 | } |
---|
| 2963 | if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) { |
---|
| 2964 | setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves); |
---|
| 2965 | } |
---|
| 2966 | |
---|
| 2967 | for (uInt i = 0; i < tempAddNWaves.size(); ++i) { |
---|
[2186] | 2968 | bool found = false; |
---|
| 2969 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
[2411] | 2970 | if (nWaves[j] == tempAddNWaves[i]) { |
---|
[2186] | 2971 | found = true; |
---|
| 2972 | break; |
---|
| 2973 | } |
---|
| 2974 | } |
---|
[2411] | 2975 | if (!found) nWaves.push_back(tempAddNWaves[i]); |
---|
[2186] | 2976 | } |
---|
| 2977 | |
---|
[2411] | 2978 | for (uInt i = 0; i < tempRejectNWaves.size(); ++i) { |
---|
[2186] | 2979 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
[2411] | 2980 | if (*j == tempRejectNWaves[i]) { |
---|
[2186] | 2981 | j = nWaves.erase(j); |
---|
| 2982 | } else { |
---|
| 2983 | ++j; |
---|
| 2984 | } |
---|
| 2985 | } |
---|
| 2986 | } |
---|
| 2987 | |
---|
| 2988 | if (nWaves.size() > 1) { |
---|
| 2989 | sort(nWaves.begin(), nWaves.end()); |
---|
| 2990 | unique(nWaves.begin(), nWaves.end()); |
---|
| 2991 | } |
---|
| 2992 | } |
---|
| 2993 | |
---|
[2411] | 2994 | void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves) |
---|
| 2995 | { |
---|
| 2996 | if ((nWaves.size() == 2)&&(nWaves[1] == -999)) { |
---|
| 2997 | int val = nWaves[0]; |
---|
| 2998 | int nyquistFreq = nchan(getIF(whichrow))/2+1; |
---|
| 2999 | nWaves.clear(); |
---|
| 3000 | if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759 |
---|
| 3001 | nWaves.push_back(0); |
---|
| 3002 | } |
---|
| 3003 | while (val <= nyquistFreq) { |
---|
| 3004 | nWaves.push_back(val); |
---|
| 3005 | val++; |
---|
| 3006 | } |
---|
| 3007 | } |
---|
| 3008 | } |
---|
| 3009 | |
---|
[2189] | 3010 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2186] | 3011 | { |
---|
[2193] | 3012 | try { |
---|
| 3013 | ofstream ofs; |
---|
| 3014 | String coordInfo = ""; |
---|
| 3015 | bool hasSameNchan = true; |
---|
| 3016 | bool outTextFile = false; |
---|
[2640] | 3017 | bool csvFormat = false; |
---|
[2012] | 3018 | |
---|
[2193] | 3019 | if (blfile != "") { |
---|
[2640] | 3020 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3021 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 3022 | if (ofs) outTextFile = true; |
---|
| 3023 | } |
---|
[2012] | 3024 | |
---|
[2193] | 3025 | if (outLogger || outTextFile) { |
---|
| 3026 | coordInfo = getCoordInfo()[0]; |
---|
| 3027 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3028 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3029 | } |
---|
[2012] | 3030 | |
---|
[2193] | 3031 | //Fitter fitter = Fitter(); |
---|
| 3032 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 3033 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 3034 | |
---|
[2193] | 3035 | int nRow = nrow(); |
---|
| 3036 | std::vector<bool> chanMask; |
---|
| 3037 | std::vector<int> nWaves; |
---|
[2012] | 3038 | |
---|
[2193] | 3039 | bool showProgress; |
---|
| 3040 | int minNRow; |
---|
| 3041 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 3042 | |
---|
[2193] | 3043 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 3044 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 3045 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
[2186] | 3046 | |
---|
[2193] | 3047 | //FOR DEBUGGING------------ |
---|
[2411] | 3048 | /* |
---|
[2193] | 3049 | if (whichrow < 0) {// == nRow -1) { |
---|
| 3050 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow); |
---|
| 3051 | if (applyFFT) { |
---|
[2186] | 3052 | cout << "[ "; |
---|
| 3053 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
| 3054 | cout << nWaves[j] << ", "; |
---|
| 3055 | } |
---|
| 3056 | cout << " ] " << endl; |
---|
[2193] | 3057 | } |
---|
| 3058 | cout << flush; |
---|
[2186] | 3059 | } |
---|
[2411] | 3060 | */ |
---|
[2193] | 3061 | //------------------------- |
---|
| 3062 | |
---|
| 3063 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 3064 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 3065 | std::vector<float> params; |
---|
| 3066 | int nClipped = 0; |
---|
| 3067 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 3068 | setSpectrum(res, whichrow); |
---|
| 3069 | // |
---|
| 3070 | |
---|
[2640] | 3071 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped); |
---|
[2193] | 3072 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2186] | 3073 | } |
---|
| 3074 | |
---|
[2193] | 3075 | if (outTextFile) ofs.close(); |
---|
[2012] | 3076 | |
---|
[2193] | 3077 | } catch (...) { |
---|
| 3078 | throw; |
---|
[1931] | 3079 | } |
---|
[1907] | 3080 | } |
---|
| 3081 | |
---|
[2189] | 3082 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 3083 | { |
---|
[2193] | 3084 | try { |
---|
| 3085 | ofstream ofs; |
---|
| 3086 | String coordInfo = ""; |
---|
| 3087 | bool hasSameNchan = true; |
---|
| 3088 | bool outTextFile = false; |
---|
[2640] | 3089 | bool csvFormat = false; |
---|
[2012] | 3090 | |
---|
[2193] | 3091 | if (blfile != "") { |
---|
[2640] | 3092 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3093 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 3094 | if (ofs) outTextFile = true; |
---|
| 3095 | } |
---|
[2012] | 3096 | |
---|
[2193] | 3097 | if (outLogger || outTextFile) { |
---|
| 3098 | coordInfo = getCoordInfo()[0]; |
---|
| 3099 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3100 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3101 | } |
---|
[2012] | 3102 | |
---|
[2193] | 3103 | //Fitter fitter = Fitter(); |
---|
| 3104 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 3105 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 3106 | |
---|
[2193] | 3107 | int nRow = nrow(); |
---|
| 3108 | std::vector<bool> chanMask; |
---|
| 3109 | std::vector<int> nWaves; |
---|
[2186] | 3110 | |
---|
[2193] | 3111 | int minEdgeSize = getIFNos().size()*2; |
---|
| 3112 | STLineFinder lineFinder = STLineFinder(); |
---|
| 3113 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 3114 | |
---|
[2193] | 3115 | bool showProgress; |
---|
| 3116 | int minNRow; |
---|
| 3117 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 3118 | |
---|
[2193] | 3119 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 3120 | |
---|
[2193] | 3121 | //------------------------------------------------------- |
---|
| 3122 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 3123 | //------------------------------------------------------- |
---|
| 3124 | int edgeSize = edge.size(); |
---|
| 3125 | std::vector<int> currentEdge; |
---|
| 3126 | if (edgeSize >= 2) { |
---|
| 3127 | int idx = 0; |
---|
| 3128 | if (edgeSize > 2) { |
---|
| 3129 | if (edgeSize < minEdgeSize) { |
---|
| 3130 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3131 | } |
---|
| 3132 | idx = 2 * getIF(whichrow); |
---|
[2012] | 3133 | } |
---|
[2193] | 3134 | currentEdge.push_back(edge[idx]); |
---|
| 3135 | currentEdge.push_back(edge[idx+1]); |
---|
| 3136 | } else { |
---|
| 3137 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 3138 | } |
---|
[2193] | 3139 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 3140 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 3141 | chanMask = lineFinder.getMask(); |
---|
| 3142 | //------------------------------------------------------- |
---|
| 3143 | |
---|
| 3144 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
| 3145 | |
---|
| 3146 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 3147 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 3148 | std::vector<float> params; |
---|
| 3149 | int nClipped = 0; |
---|
| 3150 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 3151 | setSpectrum(res, whichrow); |
---|
| 3152 | // |
---|
| 3153 | |
---|
[2640] | 3154 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped); |
---|
[2193] | 3155 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2012] | 3156 | } |
---|
| 3157 | |
---|
[2193] | 3158 | if (outTextFile) ofs.close(); |
---|
[2012] | 3159 | |
---|
[2193] | 3160 | } catch (...) { |
---|
| 3161 | throw; |
---|
[2047] | 3162 | } |
---|
| 3163 | } |
---|
| 3164 | |
---|
[2193] | 3165 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 3166 | { |
---|
[2047] | 3167 | if (data.size() != mask.size()) { |
---|
[2081] | 3168 | throw(AipsError("data and mask sizes are not identical")); |
---|
[2047] | 3169 | } |
---|
[2081] | 3170 | if (data.size() < 2) { |
---|
| 3171 | throw(AipsError("data size is too short")); |
---|
| 3172 | } |
---|
| 3173 | if (waveNumbers.size() == 0) { |
---|
[2186] | 3174 | throw(AipsError("no wave numbers given")); |
---|
[2081] | 3175 | } |
---|
| 3176 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
| 3177 | nWaves.reserve(waveNumbers.size()); |
---|
| 3178 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
| 3179 | sort(nWaves.begin(), nWaves.end()); |
---|
| 3180 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
| 3181 | nWaves.erase(end_it, nWaves.end()); |
---|
| 3182 | |
---|
| 3183 | int minNWaves = nWaves[0]; |
---|
| 3184 | if (minNWaves < 0) { |
---|
[2058] | 3185 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
| 3186 | } |
---|
[2081] | 3187 | bool hasConstantTerm = (minNWaves == 0); |
---|
[2047] | 3188 | |
---|
| 3189 | int nChan = data.size(); |
---|
| 3190 | std::vector<int> maskArray; |
---|
| 3191 | std::vector<int> x; |
---|
| 3192 | for (int i = 0; i < nChan; ++i) { |
---|
| 3193 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 3194 | if (mask[i]) { |
---|
| 3195 | x.push_back(i); |
---|
| 3196 | } |
---|
| 3197 | } |
---|
| 3198 | |
---|
[2081] | 3199 | int initNData = x.size(); |
---|
[2047] | 3200 | |
---|
[2081] | 3201 | int nData = initNData; |
---|
| 3202 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
| 3203 | |
---|
| 3204 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
[2186] | 3205 | double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK) |
---|
[2081] | 3206 | |
---|
| 3207 | // xArray : contains elemental values for computing the least-square matrix. |
---|
| 3208 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
| 3209 | // Each xArray element are as follows: |
---|
| 3210 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
| 3211 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])}, |
---|
| 3212 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])}, |
---|
| 3213 | // where (1 <= n <= nMaxWavesInSW), |
---|
| 3214 | // or, |
---|
| 3215 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])}, |
---|
| 3216 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])}, |
---|
| 3217 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
| 3218 | std::vector<std::vector<double> > xArray; |
---|
| 3219 | if (hasConstantTerm) { |
---|
| 3220 | std::vector<double> xu; |
---|
| 3221 | for (int j = 0; j < nChan; ++j) { |
---|
| 3222 | xu.push_back(1.0); |
---|
| 3223 | } |
---|
| 3224 | xArray.push_back(xu); |
---|
| 3225 | } |
---|
| 3226 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
| 3227 | double xFactor = baseXFactor*(double)nWaves[i]; |
---|
| 3228 | std::vector<double> xs, xc; |
---|
| 3229 | xs.clear(); |
---|
| 3230 | xc.clear(); |
---|
| 3231 | for (int j = 0; j < nChan; ++j) { |
---|
| 3232 | xs.push_back(sin(xFactor*(double)j)); |
---|
| 3233 | xc.push_back(cos(xFactor*(double)j)); |
---|
| 3234 | } |
---|
| 3235 | xArray.push_back(xs); |
---|
| 3236 | xArray.push_back(xc); |
---|
| 3237 | } |
---|
| 3238 | |
---|
| 3239 | std::vector<double> z1, r1, residual; |
---|
[2047] | 3240 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3241 | z1.push_back((double)data[i]); |
---|
[2047] | 3242 | r1.push_back(0.0); |
---|
[2081] | 3243 | residual.push_back(0.0); |
---|
[2047] | 3244 | } |
---|
| 3245 | |
---|
| 3246 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2081] | 3247 | // xMatrix : horizontal concatenation of |
---|
| 3248 | // the least-sq. matrix (left) and an |
---|
| 3249 | // identity matrix (right). |
---|
| 3250 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2047] | 3251 | double xMatrix[nDOF][2*nDOF]; |
---|
| 3252 | double zMatrix[nDOF]; |
---|
| 3253 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3254 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 3255 | xMatrix[i][j] = 0.0; |
---|
[2012] | 3256 | } |
---|
[2047] | 3257 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 3258 | zMatrix[i] = 0.0; |
---|
| 3259 | } |
---|
| 3260 | |
---|
[2193] | 3261 | int nUseData = 0; |
---|
[2081] | 3262 | for (int k = 0; k < nChan; ++k) { |
---|
| 3263 | if (maskArray[k] == 0) continue; |
---|
| 3264 | |
---|
| 3265 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3266 | for (int j = i; j < nDOF; ++j) { |
---|
| 3267 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
| 3268 | } |
---|
| 3269 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
| 3270 | } |
---|
[2193] | 3271 | |
---|
| 3272 | nUseData++; |
---|
[2047] | 3273 | } |
---|
| 3274 | |
---|
[2193] | 3275 | if (nUseData < 1) { |
---|
| 3276 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
| 3277 | } |
---|
| 3278 | |
---|
[2047] | 3279 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3280 | for (int j = 0; j < i; ++j) { |
---|
| 3281 | xMatrix[i][j] = xMatrix[j][i]; |
---|
[2012] | 3282 | } |
---|
| 3283 | } |
---|
| 3284 | |
---|
[2047] | 3285 | std::vector<double> invDiag; |
---|
| 3286 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3287 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 3288 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3289 | xMatrix[i][j] *= invDiag[i]; |
---|
| 3290 | } |
---|
| 3291 | } |
---|
| 3292 | |
---|
| 3293 | for (int k = 0; k < nDOF; ++k) { |
---|
| 3294 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3295 | if (i != k) { |
---|
| 3296 | double factor1 = xMatrix[k][k]; |
---|
| 3297 | double factor2 = xMatrix[i][k]; |
---|
| 3298 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3299 | xMatrix[i][j] *= factor1; |
---|
| 3300 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 3301 | xMatrix[i][j] /= factor1; |
---|
| 3302 | } |
---|
| 3303 | } |
---|
| 3304 | } |
---|
| 3305 | double xDiag = xMatrix[k][k]; |
---|
| 3306 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3307 | xMatrix[k][j] /= xDiag; |
---|
| 3308 | } |
---|
| 3309 | } |
---|
| 3310 | |
---|
| 3311 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3312 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3313 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 3314 | } |
---|
| 3315 | } |
---|
| 3316 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
[2081] | 3317 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
| 3318 | //and cosine functions, respectively. |
---|
[2047] | 3319 | std::vector<double> y; |
---|
[2081] | 3320 | params.clear(); |
---|
[2047] | 3321 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3322 | y.push_back(0.0); |
---|
| 3323 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3324 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 3325 | } |
---|
[2081] | 3326 | params.push_back(y[i]); |
---|
[2047] | 3327 | } |
---|
| 3328 | |
---|
| 3329 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3330 | r1[i] = y[0]; |
---|
| 3331 | for (int j = 1; j < nDOF; ++j) { |
---|
| 3332 | r1[i] += y[j]*xArray[j][i]; |
---|
| 3333 | } |
---|
| 3334 | residual[i] = z1[i] - r1[i]; |
---|
[2047] | 3335 | } |
---|
| 3336 | |
---|
| 3337 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 3338 | break; |
---|
| 3339 | } else { |
---|
| 3340 | double stdDev = 0.0; |
---|
| 3341 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3342 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2047] | 3343 | } |
---|
| 3344 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 3345 | |
---|
| 3346 | double thres = stdDev * thresClip; |
---|
| 3347 | int newNData = 0; |
---|
| 3348 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3349 | if (abs(residual[i]) >= thres) { |
---|
[2047] | 3350 | maskArray[i] = 0; |
---|
| 3351 | } |
---|
| 3352 | if (maskArray[i] > 0) { |
---|
| 3353 | newNData++; |
---|
| 3354 | } |
---|
| 3355 | } |
---|
[2081] | 3356 | if (newNData == nData) { |
---|
| 3357 | break; //no more flag to add. iteration stops. |
---|
[2047] | 3358 | } else { |
---|
[2081] | 3359 | nData = newNData; |
---|
[2047] | 3360 | } |
---|
| 3361 | } |
---|
[2012] | 3362 | } |
---|
| 3363 | |
---|
[2193] | 3364 | nClipped = initNData - nData; |
---|
| 3365 | |
---|
[2058] | 3366 | std::vector<float> result; |
---|
| 3367 | if (getResidual) { |
---|
| 3368 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3369 | result.push_back((float)residual[i]); |
---|
[2058] | 3370 | } |
---|
| 3371 | } else { |
---|
| 3372 | for (int i = 0; i < nChan; ++i) { |
---|
| 3373 | result.push_back((float)r1[i]); |
---|
| 3374 | } |
---|
[2047] | 3375 | } |
---|
| 3376 | |
---|
[2058] | 3377 | return result; |
---|
[2012] | 3378 | } |
---|
| 3379 | |
---|
[2047] | 3380 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
| 3381 | { |
---|
[2081] | 3382 | std::vector<double> dAbcissa = getAbcissa(whichrow); |
---|
| 3383 | std::vector<float> abcissa; |
---|
| 3384 | for (uInt i = 0; i < dAbcissa.size(); ++i) { |
---|
| 3385 | abcissa.push_back((float)dAbcissa[i]); |
---|
[2047] | 3386 | } |
---|
| 3387 | std::vector<float> spec = getSpectrum(whichrow); |
---|
[2012] | 3388 | |
---|
[2081] | 3389 | fitter.setData(abcissa, spec, mask); |
---|
[2047] | 3390 | fitter.lfit(); |
---|
| 3391 | } |
---|
| 3392 | |
---|
| 3393 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
| 3394 | { |
---|
[2186] | 3395 | std::vector<bool> mask = getMask(whichrow); |
---|
| 3396 | uInt maskSize = mask.size(); |
---|
[2410] | 3397 | if (inMask.size() != 0) { |
---|
| 3398 | if (maskSize != inMask.size()) { |
---|
| 3399 | throw(AipsError("mask sizes are not the same.")); |
---|
| 3400 | } |
---|
| 3401 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 3402 | mask[i] = mask[i] && inMask[i]; |
---|
| 3403 | } |
---|
[2047] | 3404 | } |
---|
| 3405 | |
---|
[2186] | 3406 | return mask; |
---|
[2047] | 3407 | } |
---|
| 3408 | |
---|
| 3409 | /* |
---|
| 3410 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
| 3411 | { |
---|
| 3412 | int edgeSize = edge.size(); |
---|
| 3413 | std::vector<int> currentEdge; |
---|
| 3414 | if (edgeSize >= 2) { |
---|
| 3415 | int idx = 0; |
---|
| 3416 | if (edgeSize > 2) { |
---|
| 3417 | if (edgeSize < minEdgeSize) { |
---|
| 3418 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3419 | } |
---|
| 3420 | idx = 2 * getIF(whichrow); |
---|
| 3421 | } |
---|
| 3422 | currentEdge.push_back(edge[idx]); |
---|
| 3423 | currentEdge.push_back(edge[idx+1]); |
---|
| 3424 | } else { |
---|
| 3425 | throw(AipsError("Wrong length of edge element")); |
---|
| 3426 | } |
---|
| 3427 | |
---|
| 3428 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 3429 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
| 3430 | |
---|
| 3431 | return lineFinder.getMask(); |
---|
| 3432 | } |
---|
| 3433 | */ |
---|
| 3434 | |
---|
| 3435 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
[2640] | 3436 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter) |
---|
[2186] | 3437 | { |
---|
[2047] | 3438 | if (outLogger || outTextFile) { |
---|
| 3439 | std::vector<float> params = fitter.getParameters(); |
---|
| 3440 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
| 3441 | float rms = getRms(chanMask, whichrow); |
---|
| 3442 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 3443 | |
---|
| 3444 | if (outLogger) { |
---|
| 3445 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2640] | 3446 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 3447 | } |
---|
| 3448 | if (outTextFile) { |
---|
[2640] | 3449 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 3450 | } |
---|
| 3451 | } |
---|
| 3452 | } |
---|
| 3453 | |
---|
| 3454 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
[2640] | 3455 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped) |
---|
[2186] | 3456 | { |
---|
[2047] | 3457 | if (outLogger || outTextFile) { |
---|
| 3458 | float rms = getRms(chanMask, whichrow); |
---|
| 3459 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 3460 | std::vector<bool> fixed; |
---|
| 3461 | fixed.clear(); |
---|
[2047] | 3462 | |
---|
| 3463 | if (outLogger) { |
---|
| 3464 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2640] | 3465 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 3466 | } |
---|
| 3467 | if (outTextFile) { |
---|
[2640] | 3468 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 3469 | } |
---|
| 3470 | } |
---|
| 3471 | } |
---|
| 3472 | |
---|
| 3473 | /* for sinusoid. will be merged once sinusoid is available in fitter (2011/3/10 WK) */ |
---|
[2640] | 3474 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped) |
---|
[2186] | 3475 | { |
---|
[2047] | 3476 | if (outLogger || outTextFile) { |
---|
| 3477 | float rms = getRms(chanMask, whichrow); |
---|
| 3478 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 3479 | std::vector<bool> fixed; |
---|
| 3480 | fixed.clear(); |
---|
[2047] | 3481 | |
---|
| 3482 | if (outLogger) { |
---|
| 3483 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2640] | 3484 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 3485 | } |
---|
| 3486 | if (outTextFile) { |
---|
[2640] | 3487 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 3488 | } |
---|
| 3489 | } |
---|
| 3490 | } |
---|
| 3491 | |
---|
[2189] | 3492 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
[2186] | 3493 | { |
---|
[2189] | 3494 | int idxDelimiter = progressInfo.find(","); |
---|
| 3495 | if (idxDelimiter < 0) { |
---|
| 3496 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
| 3497 | } |
---|
| 3498 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
| 3499 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
| 3500 | is >> minNRow; |
---|
| 3501 | } |
---|
| 3502 | |
---|
| 3503 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
| 3504 | { |
---|
| 3505 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
[2186] | 3506 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
| 3507 | if (nInterval == 0) nInterval++; |
---|
| 3508 | |
---|
[2193] | 3509 | if (nProcessed % nInterval == 0) { |
---|
[2189] | 3510 | printf("\r"); //go to the head of line |
---|
[2186] | 3511 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
[2189] | 3512 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
| 3513 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
[2186] | 3514 | fflush(NULL); |
---|
| 3515 | } |
---|
[2193] | 3516 | |
---|
[2186] | 3517 | if (nProcessed == nTotal - 1) { |
---|
| 3518 | printf("\r\x1b[K"); //clear |
---|
| 3519 | fflush(NULL); |
---|
| 3520 | } |
---|
[2193] | 3521 | |
---|
[2186] | 3522 | } |
---|
| 3523 | } |
---|
| 3524 | |
---|
| 3525 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
| 3526 | { |
---|
| 3527 | std::vector<bool> mask = getMask(whichrow); |
---|
| 3528 | |
---|
| 3529 | if (inMask.size() > 0) { |
---|
| 3530 | uInt maskSize = mask.size(); |
---|
| 3531 | if (maskSize != inMask.size()) { |
---|
| 3532 | throw(AipsError("mask sizes are not the same.")); |
---|
| 3533 | } |
---|
| 3534 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 3535 | mask[i] = mask[i] && inMask[i]; |
---|
| 3536 | } |
---|
| 3537 | } |
---|
| 3538 | |
---|
| 3539 | Vector<Float> spec = getSpectrum(whichrow); |
---|
| 3540 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
| 3541 | |
---|
| 3542 | FFTServer<Float,Complex> ffts; |
---|
| 3543 | Vector<Complex> fftres; |
---|
| 3544 | ffts.fft0(fftres, spec); |
---|
| 3545 | |
---|
| 3546 | std::vector<float> res; |
---|
| 3547 | float norm = float(2.0/double(spec.size())); |
---|
| 3548 | |
---|
| 3549 | if (getRealImag) { |
---|
| 3550 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 3551 | res.push_back(real(fftres[i])*norm); |
---|
| 3552 | res.push_back(imag(fftres[i])*norm); |
---|
| 3553 | } |
---|
| 3554 | } else { |
---|
| 3555 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 3556 | res.push_back(abs(fftres[i])*norm); |
---|
| 3557 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
| 3558 | } |
---|
| 3559 | } |
---|
| 3560 | |
---|
| 3561 | return res; |
---|
| 3562 | } |
---|
| 3563 | |
---|
| 3564 | |
---|
| 3565 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
| 3566 | { |
---|
[2012] | 3567 | Vector<Float> spec; |
---|
| 3568 | specCol_.get(whichrow, spec); |
---|
| 3569 | |
---|
| 3570 | float mean = 0.0; |
---|
| 3571 | float smean = 0.0; |
---|
| 3572 | int n = 0; |
---|
[2047] | 3573 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
[2012] | 3574 | if (mask[i]) { |
---|
| 3575 | mean += spec[i]; |
---|
| 3576 | smean += spec[i]*spec[i]; |
---|
| 3577 | n++; |
---|
| 3578 | } |
---|
| 3579 | } |
---|
| 3580 | |
---|
| 3581 | mean /= (float)n; |
---|
| 3582 | smean /= (float)n; |
---|
| 3583 | |
---|
| 3584 | return sqrt(smean - mean*mean); |
---|
| 3585 | } |
---|
| 3586 | |
---|
| 3587 | |
---|
[2640] | 3588 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const |
---|
[2012] | 3589 | { |
---|
[2640] | 3590 | if (verbose) { |
---|
| 3591 | ostringstream oss; |
---|
[2012] | 3592 | |
---|
[2640] | 3593 | if (csvformat) { |
---|
| 3594 | oss << getScan(whichrow) << ","; |
---|
| 3595 | oss << getBeam(whichrow) << ","; |
---|
| 3596 | oss << getIF(whichrow) << ","; |
---|
| 3597 | oss << getPol(whichrow) << ","; |
---|
| 3598 | oss << getCycle(whichrow) << ","; |
---|
| 3599 | String commaReplacedMasklist = masklist; |
---|
| 3600 | string::size_type pos = 0; |
---|
| 3601 | while (pos = commaReplacedMasklist.find(","), pos != string::npos) { |
---|
| 3602 | commaReplacedMasklist.replace(pos, 1, ";"); |
---|
| 3603 | pos++; |
---|
| 3604 | } |
---|
| 3605 | oss << commaReplacedMasklist << ","; |
---|
| 3606 | } else { |
---|
| 3607 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
| 3608 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
| 3609 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
| 3610 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
| 3611 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
| 3612 | oss << "Fitter range = " << masklist << endl; |
---|
| 3613 | oss << "Baseline parameters" << endl; |
---|
| 3614 | } |
---|
[2012] | 3615 | oss << flush; |
---|
[2640] | 3616 | |
---|
| 3617 | return String(oss); |
---|
[2012] | 3618 | } |
---|
| 3619 | |
---|
[2640] | 3620 | return ""; |
---|
[2012] | 3621 | } |
---|
| 3622 | |
---|
[2640] | 3623 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const |
---|
[2012] | 3624 | { |
---|
[2640] | 3625 | if (verbose) { |
---|
| 3626 | ostringstream oss; |
---|
[2012] | 3627 | |
---|
[2640] | 3628 | if (csvformat) { |
---|
| 3629 | oss << rms << ","; |
---|
| 3630 | if (nClipped >= 0) { |
---|
| 3631 | oss << nClipped; |
---|
| 3632 | } |
---|
| 3633 | } else { |
---|
| 3634 | oss << endl; |
---|
| 3635 | oss << "Results of baseline fit" << endl; |
---|
| 3636 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
| 3637 | if (nClipped >= 0) { |
---|
| 3638 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
| 3639 | } |
---|
| 3640 | for (int i = 0; i < 60; ++i) { |
---|
| 3641 | oss << "-"; |
---|
| 3642 | } |
---|
[2193] | 3643 | } |
---|
[2131] | 3644 | oss << endl; |
---|
[2094] | 3645 | oss << flush; |
---|
[2640] | 3646 | |
---|
| 3647 | return String(oss); |
---|
[2012] | 3648 | } |
---|
| 3649 | |
---|
[2640] | 3650 | return ""; |
---|
[2012] | 3651 | } |
---|
| 3652 | |
---|
[2186] | 3653 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
| 3654 | const std::vector<bool>& fixed, |
---|
| 3655 | float rms, |
---|
[2193] | 3656 | int nClipped, |
---|
[2186] | 3657 | const std::string& masklist, |
---|
| 3658 | int whichrow, |
---|
| 3659 | bool verbose, |
---|
[2640] | 3660 | bool csvformat, |
---|
[2186] | 3661 | int start, int count, |
---|
| 3662 | bool resetparamid) const |
---|
[2047] | 3663 | { |
---|
[2064] | 3664 | int nParam = (int)(params.size()); |
---|
[2047] | 3665 | |
---|
[2064] | 3666 | if (nParam < 1) { |
---|
| 3667 | return(" Not fitted"); |
---|
| 3668 | } else { |
---|
| 3669 | |
---|
| 3670 | ostringstream oss; |
---|
[2640] | 3671 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
[2064] | 3672 | |
---|
| 3673 | if (start < 0) start = 0; |
---|
| 3674 | if (count < 0) count = nParam; |
---|
| 3675 | int end = start + count; |
---|
| 3676 | if (end > nParam) end = nParam; |
---|
| 3677 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
| 3678 | |
---|
| 3679 | for (int i = start; i < end; ++i) { |
---|
| 3680 | if (i > start) { |
---|
[2047] | 3681 | oss << ","; |
---|
| 3682 | } |
---|
[2064] | 3683 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
[2640] | 3684 | if (csvformat) { |
---|
| 3685 | oss << params[i] << sFix; |
---|
| 3686 | } else { |
---|
| 3687 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
| 3688 | } |
---|
[2047] | 3689 | } |
---|
[2064] | 3690 | |
---|
[2640] | 3691 | if (csvformat) { |
---|
| 3692 | oss << ","; |
---|
| 3693 | } |
---|
| 3694 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
[2064] | 3695 | |
---|
| 3696 | return String(oss); |
---|
[2047] | 3697 | } |
---|
| 3698 | |
---|
| 3699 | } |
---|
| 3700 | |
---|
[2640] | 3701 | std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose, bool csvformat) const |
---|
[2012] | 3702 | { |
---|
[2064] | 3703 | int nOutParam = (int)(params.size()); |
---|
| 3704 | int nPiece = (int)(ranges.size()) - 1; |
---|
[2012] | 3705 | |
---|
[2064] | 3706 | if (nOutParam < 1) { |
---|
| 3707 | return(" Not fitted"); |
---|
| 3708 | } else if (nPiece < 0) { |
---|
[2640] | 3709 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat); |
---|
[2064] | 3710 | } else if (nPiece < 1) { |
---|
| 3711 | return(" Bad count of the piece edge info"); |
---|
| 3712 | } else if (nOutParam % nPiece != 0) { |
---|
| 3713 | return(" Bad count of the output baseline parameters"); |
---|
| 3714 | } else { |
---|
| 3715 | |
---|
| 3716 | int nParam = nOutParam / nPiece; |
---|
| 3717 | |
---|
| 3718 | ostringstream oss; |
---|
[2640] | 3719 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
[2064] | 3720 | |
---|
[2640] | 3721 | if (csvformat) { |
---|
| 3722 | for (int i = 0; i < nPiece; ++i) { |
---|
| 3723 | oss << ranges[i] << "," << (ranges[i+1]-1) << ","; |
---|
| 3724 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
| 3725 | } |
---|
| 3726 | } else { |
---|
| 3727 | stringstream ss; |
---|
| 3728 | ss << ranges[nPiece] << flush; |
---|
| 3729 | int wRange = ss.str().size() * 2 + 5; |
---|
[2064] | 3730 | |
---|
[2640] | 3731 | for (int i = 0; i < nPiece; ++i) { |
---|
| 3732 | ss.str(""); |
---|
| 3733 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
| 3734 | oss << left << setw(wRange) << ss.str(); |
---|
| 3735 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
| 3736 | oss << endl; |
---|
| 3737 | } |
---|
[2012] | 3738 | } |
---|
[2064] | 3739 | |
---|
[2640] | 3740 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
[2064] | 3741 | |
---|
| 3742 | return String(oss); |
---|
[2012] | 3743 | } |
---|
| 3744 | |
---|
| 3745 | } |
---|
| 3746 | |
---|
[2047] | 3747 | bool Scantable::hasSameNchanOverIFs() |
---|
[2012] | 3748 | { |
---|
[2047] | 3749 | int nIF = nif(-1); |
---|
| 3750 | int nCh; |
---|
| 3751 | int totalPositiveNChan = 0; |
---|
| 3752 | int nPositiveNChan = 0; |
---|
[2012] | 3753 | |
---|
[2047] | 3754 | for (int i = 0; i < nIF; ++i) { |
---|
| 3755 | nCh = nchan(i); |
---|
| 3756 | if (nCh > 0) { |
---|
| 3757 | totalPositiveNChan += nCh; |
---|
| 3758 | nPositiveNChan++; |
---|
[2012] | 3759 | } |
---|
| 3760 | } |
---|
| 3761 | |
---|
[2047] | 3762 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
[2012] | 3763 | } |
---|
| 3764 | |
---|
[2047] | 3765 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
[2012] | 3766 | { |
---|
[2427] | 3767 | if (mask.size() <= 0) { |
---|
| 3768 | throw(AipsError("The mask elements should be > 0")); |
---|
[2012] | 3769 | } |
---|
[2047] | 3770 | int IF = getIF(whichrow); |
---|
| 3771 | if (mask.size() != (uInt)nchan(IF)) { |
---|
[2012] | 3772 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
| 3773 | } |
---|
| 3774 | |
---|
[2047] | 3775 | if (verbose) { |
---|
[2012] | 3776 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
| 3777 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
| 3778 | if (!hasSameNchan) { |
---|
[2047] | 3779 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
[2012] | 3780 | } |
---|
| 3781 | logOs << LogIO::POST; |
---|
| 3782 | } |
---|
| 3783 | |
---|
| 3784 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
[2047] | 3785 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
| 3786 | |
---|
[2012] | 3787 | ostringstream oss; |
---|
| 3788 | oss.setf(ios::fixed); |
---|
| 3789 | oss << setprecision(1) << "["; |
---|
[2047] | 3790 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
[2012] | 3791 | if (i > 0) oss << ","; |
---|
[2047] | 3792 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
[2012] | 3793 | } |
---|
| 3794 | oss << "]" << flush; |
---|
| 3795 | |
---|
| 3796 | return String(oss); |
---|
| 3797 | } |
---|
| 3798 | |
---|
[2047] | 3799 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
[2012] | 3800 | { |
---|
[2427] | 3801 | if (mask.size() <= 0) { |
---|
| 3802 | throw(AipsError("The mask elements should be > 0")); |
---|
[2012] | 3803 | } |
---|
| 3804 | |
---|
[2047] | 3805 | std::vector<int> out, startIndices, endIndices; |
---|
| 3806 | int maskSize = mask.size(); |
---|
[2012] | 3807 | |
---|
[2047] | 3808 | startIndices.clear(); |
---|
| 3809 | endIndices.clear(); |
---|
| 3810 | |
---|
| 3811 | if (mask[0]) { |
---|
| 3812 | startIndices.push_back(0); |
---|
[2012] | 3813 | } |
---|
[2047] | 3814 | for (int i = 1; i < maskSize; ++i) { |
---|
| 3815 | if ((!mask[i-1]) && mask[i]) { |
---|
| 3816 | startIndices.push_back(i); |
---|
| 3817 | } else if (mask[i-1] && (!mask[i])) { |
---|
| 3818 | endIndices.push_back(i-1); |
---|
| 3819 | } |
---|
[2012] | 3820 | } |
---|
[2047] | 3821 | if (mask[maskSize-1]) { |
---|
| 3822 | endIndices.push_back(maskSize-1); |
---|
| 3823 | } |
---|
[2012] | 3824 | |
---|
[2047] | 3825 | if (startIndices.size() != endIndices.size()) { |
---|
| 3826 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
| 3827 | } |
---|
| 3828 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 3829 | if (startIndices[i] > endIndices[i]) { |
---|
| 3830 | throw(AipsError("Mask start index > mask end index")); |
---|
[2012] | 3831 | } |
---|
| 3832 | } |
---|
| 3833 | |
---|
[2047] | 3834 | out.clear(); |
---|
| 3835 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 3836 | out.push_back(startIndices[i]); |
---|
| 3837 | out.push_back(endIndices[i]); |
---|
| 3838 | } |
---|
| 3839 | |
---|
[2012] | 3840 | return out; |
---|
| 3841 | } |
---|
| 3842 | |
---|
[2161] | 3843 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
| 3844 | { |
---|
| 3845 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
| 3846 | vector<float> stlTsys ; |
---|
| 3847 | tsys.tovector( stlTsys ) ; |
---|
| 3848 | return stlTsys ; |
---|
| 3849 | } |
---|
[2012] | 3850 | |
---|
| 3851 | |
---|
[1907] | 3852 | } |
---|
[1819] | 3853 | //namespace asap |
---|